Characterization of a Novel Putative S-Adenosylmethionine Decarboxylase-Like Protein from Leishmania donovani
Pratap JV (2013) Characterization of a Novel Putative S-Adenosylmethionine Decarboxylase-Like Protein from Leishmania donovani. PLoS
ONE 8(6): e65912. doi:10.1371/journal.pone.0065912
Characterization of a Novel Putative S-Adenosylmethionine Decarboxylase-Like Protein from Leishmania donovani
Saurabh Pratap Singh 0
Pragati Agnihotri 0
J. Venkatesh Pratap 0
Dan Zilberstein, Technion-Israel Institute of Technology, Israel
0 Molecular & Structural Biology Division, Central Drug Research Institute , Chattar Manzil, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh , India
In addition to the S-adenosylmethionine decarboxylase (AD) present in all organisms, trypanosomatids including Leishmania spp. possess an additional copy, annotated as the putative S-adenosylmethionine decarboxylase-like proenzyme (ADL). Phylogenetic analysis confirms that ADL is unique to trypanosomatids and has several unique features such as lack of autocatalytic cleavage and a distinct evolutionary lineage, even from trypanosomatid ADs. In Trypanosoma ADL was found to be enzymaticaly dead but plays an essential regulatory role by forming a heterodimer complex with AD. However, no structural or functional information is available about ADL from Leishmania spp. Here, in this study, we report the cloning, expression, purification, structural and functional characterization of Leishmania donovani (L. donovani) ADL using biophysical, biochemical and computational techniques. Biophysical studies show that, L. donovani ADL binds Sadenosylmethionine (SAM) and putrescine which are natural substrates of AD. Computational modeling and docking studies showed that in comparison to the ADs of other organisms including human, residues involved in putrescine binding are partially conserved while the SAM binding residues are significantly different. In silico protein-protein interaction study reveals that L. donovani ADL can interact with AD. These results indicate that L. donovani ADL posses a novel substrate binding property and may play an essential role in polyamine biosynthesis with a different mode of function from known proteins of the S-adenosylmethionine decarboxylase super family.
Funding: Funding from CSIR network projects - Genomics and Informatics Solutions for Integrating Biology (GENESIS) and Understanding the role of the Host
molecule in Parasite Infection (HOPE) is acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation
of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
Visceral Leishmaniasis or kala-azar is a one of the most
neglected diseases caused by the parasitic protozoan Leishmania. It
causes an estimated 500,000 new cases of disease and more than
50,000 deaths every year with 90% occurring in Bangladesh,
Nepal, India, Sudan, Ethiopia and Brazil . The disease is
becoming a cause of concern with the advent of HIV-leishmaniasis
co-infection . Without treatment, visceral leishmaniasis is
always fatal. The available drugs have limitations like toxicity,
difficult dosing regimens, emerging resistance and therefore new
drugs are required. The first step in a rational drug design
approach is the identification, structural and functional
characterization of proteins in pathways that are indispensable to the
pathogen and are sufficiently distinct from their human
homologues. The polyamine biosynthesis pathway in Leishmania can be
one such pathway . Polyamines such as- putrescine,
spermidine and spermine are essential components of the cell
involved in cell growth, differentiation and proliferation. One of
the two drugs certified by the US Food and Drug Administration
for the treatment of late stage African sleeping sickness caused by
Trypanosoma brucei (T. brucei) is eflorinithine, a suicide inhibitor of
ornithine decarboxylase (ODC), an enzyme in the polyamine
biosynthesis pathway , further validate the importance of this
pathway. In eukaryotes including Leishmania, putrescine is
synthesized from L-ornithine through a decarboxylation reaction
catalyzed by ODC. Subsequently, spermidine is synthesized by
the incorporation of an aminopropyl group in a reaction catalyzed
by the enzyme spermidine synthase. The aminopropyl group is
provided by decarboxylated S-adenosylmethionine, which is
produced in a reaction catalyzed by S-adenosylmethionine
decarboxylase referred here as AD. Spermidine is subsequently
conjugated with glutathione to synthesize a unique polyamine in
trypanosomatids i.e. trypanothione, which is essential for cellular
redox reactions and nucleotide synthesis .
AD (E.C 22.214.171.124) belongs to a small group of enzymes that
depend on a pyruvoyl cofactor for decarboxylation reaction. AD is
expressed as an inactive proenzyme that undergoes an
autoprocessing reaction in humans, Trypanosoma and plants .
Autoprocessing involves an internal serinolysis reaction leading
to the cleavage of the proenzyme backbone into two subunits, a
small b subunit and a large a subunit and a. The catalytic
mechanism involves the generation of a pyruvoyl group at the
Nterminus of the a chain and requires the amino acid sequence ES
as its cleavage site. The substrate S-adenosylmethionine (SAM)
binds to this pyruvoyl group through a Schiff base and the
decarboxylation reaction proceeds with the transfer of a pair of
electrons from the substrate to pyruvoyl group .
Autoprocessing as well as decarboxylation are stimulated by putrescine in
humans [19,20] but not in plants and they lack the putrescine
binding site . In T. brucei putrescine is not necessary for the
autoprocessing reaction but it stimulates the decarboxylation
reaction, although the decarboxylation reaction is not as efficient
as found in human and plant AD [12,2225]. The structural
details of the enzymes belonging to the AD super family mainly
come from crystal structures of human and potato ADs [19,21].
Although these two proteins differ in their oligomeric association,
the human AD exist as a dimer while the potato AD is monomeric,
their crystal structures reveal an identical fold comprising of a four
layer abba sandwich. Each central b sheet comprises of eight
antiparallel b strands, flanked by a helices on either side. The six a
helices observed in the monomer are all amphipathic, packed
tightly against the outer faces of the b sandwich of AD. However,
no structure of AD from any trypanosomatids has been reported
Apart from AD, trypanosomatids including Leishmania possess
another AD like protein annotated in databases as a putative
Sadenosylmethionine decarboxylase-like proenzyme, here onwards
referred as ADL (NCBI gene accession no. CBZ36337.1). The T.
brucei ADL was shown to be paralogous to AD, did not undergo
autocatalysis and could not retain its native confirmation in the
absence of AD. T. brucei ADL was also found to be enzymatically
dead, but playing a significant role as a regulatory subunit by
forming a high affinity heterodimer with AD, upregulating the
enzyme activity by ,1200 fold . Though ADL controls the
activity of AD in trypanosomatids, no information is known
regarding the mechanism of regulation or the substrate binding
aspect of ADL. ADL is proposed to have evolved through
duplication of the ancestral main AD and subsequent mutational
drift that lead to the loss of its catalytic activity but retaining its
allosteric regulatory function. The conditional knockouts of T.
brucei AD and ADL revealed that depletion of either protein led to
a reduction in the level of spermidine and trypanothione
ultimately resulting in the death of the parasite. This implies that
ADL is an essential protein for the survival of Trypanosoma [26,27].
Comparison of the pairwise amino acid sequence alignments of L.
donovani AD and ADL with human AD suggest that the ADL has a
significantly lower sequence identity (,13%) than L. donovani AD
(,25%). Further, L. donovani AD shares six residues which are
involved in SAM positioning and binding and two among the
three putrescine binding residues with the human AD. This
indicates that in comparison to AD, ADL may be a better target
for any rational drug development approach. Here, in this study
we report the cloning, expression, purification, structural and
functional characterization of L. donovani ADL, to ascertain its
viability in drug development.
Materials and Methods
Sequence and phylogenetic analysis
The amino acid sequences of ADs and ADLs of kinetoplastida,
such as L. major, L. infantum, L. donovani, L. brazilensis T. brucei and T.
cruzi were retrieved from the Swiss-Prot gene database and domain
architecture was predicted using CDD (http://www.ncbi.nlm.nih.
gov/Structure/cdd/cdd.shtml)  and the fold analyzed by
FoldIndex (http://bip.weizmann.ac.il/fldbin/findex) . The
phylogenetic tree was drawn with the help of MEGA 5.0 
by using the neighbor joining method based on the bottom-up
clustering algorithm . The sequences were aligned using
ClustalW version 1.8 . The secondary structure was predicted
by using PHD server (http://npsapbil.ibcp.fr) . The Q site
finder (http://www.modelling.leeds.ac.uk/qsitefinder/) was used
to identify conserved functional residues .
Cloning, protein expression and purification
The 894 bp long L. donovani ADL gene was amplified from the
genomic DNA of L. donovani using specific sense
5GGGAAGCTTATCTGCACTGCGGGCGAATAGTAGTTGGTG3 primers designed using Oligo software, with
sites for BamHI and HindIII restriction enzymes (underlined)
respectively. The amplified gene was cloned in T/A vector
pTZ57R/T (InsTA cloneTM PCR cloning kit, Fermentas
International Inc.) and then sub-cloned downstream of the T5
promoter expression vector pQE30 (Qiagen) between BamHI and
HindIII sites. E. coli TG1 host cell was transformed with the
recombinant plasmid pQE30-ADL and used for over-expression.
Luria-Bertani (LB) broth containing ampicillin (100 mg/ml) was
inoculated with the E. coli containing the pQE30-ADL plasmid
and cultured overnight at 37uC. Fresh LB broth containing
ampicillin (100 mg/ml) was inoculated with 1:100 dilution of this
seed culture and incubated at 37uC to an OD600 of ,0.6.
Overexpression was then induced by adding 1 mM
isopropyl-1-thio-bgalactopyranoside (IPTG) and allowed to grow overnight at the
same temperature. The culture was subsequently harvested by
centrifugation, resuspended in a buffer containing 50 mM
TrisHCl pH 7.0 and 200 mM NaCl. Cells were lysed by sonication
with a 20 second on and 15 second off pulse for 30 minutes. Cell
debris was removed by centrifugation at 13,000 rpm for 30
minutes and the supernatant loaded on an IMAC column
preequilibrated with the same buffer. The column was incubated for
an hour and subsequently washed with buffers containing 10 mM
and 60 mM imidazole. Protein was then eluted with 300 mM
imidazole in the same buffer. The eluted protein was dialyzed
overnight into 50 mM Tris-HCl pH 7.0, 50 mM NaCl, 1 mM
putrescine and 3 mM b-me, concentrated using 10 kDa cutoff
centricon (Amicon) and loaded on size exclusion chromatography
for the second step purification and oligomerization analysis.
Size exclusion chromatography
Size exclusion chromatography was performed on the
SuperdexTM 75 10/300 prepacked column (manufacturers exclusion
limit 70 kDa for proteins) on an DKTA-FPLC (GE HealthCare
Biosciences). The dialyzed and concentrated ADL protein (1 mg/
ml) was loaded onto the column pre-equilibrated with a buffer
containing 50 mM Tris-HCl pH 7.0, 50 mM NaCl, and 3 mM
bme. The elution was carried out isocratically at a flow rate of 0.3
0.4 ml/min and monitored using the absorbance at 280 nm. All
measurements were made at 25uC. Calibration of the column was
performed using the low molecular weight standard kit (GE
Healthcare) containing conalbumin, ovalbumin, carbonic
anhydrase, RNAase and aprotinine as reference proteins.
Determination of protein concentration
The protein concentration was determined by using Bradford
method . The standard curve was plotted with bovine serum
albumin in range of 022 mg/ml.
Trypsin digestion was used to analyze the domain architecture
of ADL protein. Trypsin was added to ADL in a 200:1 ratio and
reactions were set up for 10 min, 30 min, 1 hour and overnight
and, stopped by adding 1 mM PMSF. The effect of substrates such
as SAM and putrescine on limited proteolysis was observed in the
concentration range 080 mM and 090 mM respectively in an
overnight reaction. All samples were analyzed on a 12%
The fluorescence emission spectra using intrinsic (Tryptophan)
and extrinsic (1-anilinonapthelene-8-sulfonate, ANS) fluorophores
were recorded on a Perkin Elmer LS50b luminescence
spectrometer at 25uC. Cuvettes with 5 mm path length were used and
2 mM ADL in 50 mM Tris-HCl pH 7.0, 50 mM NaCl and 3 mM
b-me was used for these studies. For tryptophan fluorescence, the
protein sample was excited at 295 nm and the emission spectra
recorded in the range 300400 nm. For ANS binding studies, the
corresponding values were 370 nm and 400600 nm respectively.
For ANS binding studies, a dye to protein molar ratio of 20:1 was
used and the samples were incubated with ANS for 30 minutes
and gently shaken before taking measurements. The effect of urea
and Guanidinium chloride (GdmCl) on ADL was observed in the
concentration range 06 M by using tryptophan and ANS
fluorescence. Fluorescence spectra with increasing concentrations
of SAM and putrescine (0200 mM) up to saturation were
measured and the change in tryptophan fluorescence observed
at 341 nm. As a control, titrations with buffer alone did not
produce any significant change in the emission signal. The change
in fluorescence can be then related to the binding of SAM and
putrescine by the following equation [36,37].
Where DF is the magnitude of the difference between the
observed fluorescence intensities in the presence and absence of
the substrate at a given concentration of substrate, DFmax is the
difference between the observed fluorescence intensities at zero
and saturating substrate concentration, [Substrate] tot, and Kf is
the apparent dissociation constant. The Kd values were
determined from a non-linear least-squares regression analysis of
titration data. With all samples, fluorescence spectra were
corrected for the background fluorescence of the solution
(buffer+substrate). Deconvolution of curves was performed using
the Prism software (GraphPad software Inc) & Phase diagrams
describing GdmCl and urea induced changes of fluorescence
intensities were constructed.
Circular dichroism measurements
The far-UV CD measurements were made on a Jasco J810
spectropolarimeter and ChirascanTM CD spectropolarimeter
(Applied Photophysics) calibrated with ammonium (+)-10-
camphorsulfonate. Three spectra (200260 nm, scan-speed 10 nm/
min) from 2 mM protein samples in 50 mM Tris HCl pH 7.0,
50 mM NaCl were taken and averaged. All measurements were
taken using standard protocol . The K2D3 software (http://
www.ogic.ca/projects/k2d3/) was used to estimate the secondary
structure content of the protein . The effect of SAM and
putrescine was observed in the concentration range 0200 mM.
Secondary structure was observed in a buffer containing 50 mM
NaCl and 3 mM b-me with pH profile varying from 4.0 to 9.0 i.e.
50 mM sodium acetate pH 4.0, 50 mM MES pH 6.0, and
50 mM Tris-HCl pH 7.0 and 9.0. The thermal denaturation
experiments of L donovani ADL, in apo and in complex with SAM
and putrescine were performed in the same spectropolarimeter
using the standard protocol between 25uC90uC. The folded
fraction of the protein at these temperature values were
Homology modeling and docking studies of L donovani
In the absence of suitable template hits by PSI-BLAST against
the PDB, the templates for homology modeling were found by
searching structures with similar fold, using the PHYRE server
(http://www.sbg.bio.ic.ac.uk/,phyre/) which too takes the
amino acid sequence as input and combines predicted secondary
structure information in addition to PSI-BLAST generated
alignment profile . PHYRE identified four structures in the
PDB as potential templates with 100% confidence: three human
AD structures (in apo and liganded forms, PDB IDs 1I7B, 1MSV,
1JLO) and the structure of potato AD (PDB ID 1MHM). The
human structure was taken as the template for homology
modelling. Homology modeling was performed using
MODELLER 9.10 using default parameters with the pairwise sequence
alignment file of the target (L. donovani ADL) and the template as
input . Five models were obtained as modeller output with
each template and were ranked on the basis of their minimum
internal energy. The model with minimum internal energy and
root mean square deviation from the template was used for further
validation. The quality of these models were validated using
MolProbity and PROCHECK [43,44]. Homology models of AD
and ADL from L. major, L. infantum, L. donovani and L. brazilensis
were also made to confirm the interactions involved in
Molecular docking study was performed using docking software
AUTODOCK 3.0 with default parameters . The L. donovani
ADL model was docked with the substrates SAM and putrescine.
Ten conformations of each ligand were obtained and ranked
according to their minimum docking energies. The best
conformation selected on the basis of minimum docking energy, and no
steric clashes between the residues involved in binding. The
conformation which obeys these conditions was used for the active
site analysis. The protein-ligands interaction diagram was
generated by using LIGPLOT tool .
The protein-protein interaction was analyzed by STRING 9.0
(http://string-db.org) . STRING 9.0 is an interacting genes
database which requires gene ID or amino-acid sequence as input
and predicts interaction on the basis of genomic context,
highthroughput experiments, co-expression, experiments and previous
knowledge. Protein-protein docking was carried out independently
using two different servers, ClusPro 2.0 (http://cluspro.bu.edu/
login.php) and GRAMM-X (http://vakser.bioinformatics.ku.edu/
resources/gramm/grammx) [48,49]. While ClusPro 2.0 utilizes
the models or PDB IDs of query interacting partners as input and
performs rigid body docking to give a docked model, GRAMM-X
is based on a Fast Fourier transform algorithm utilizing shape
complementarity and a softend-Lennard-Jones potential function.
Results and Discussion
ADL belongs to the S-adenosylmethionine decarboxylase
superfamily, having a single domain as predicted by the conserved
domain prediction and FoldIndex respectively, while a BLAST
search against the non redundant protein database shows that
ADL is found only in trypanosomatids. PSI-BLAST against the
PDB did not show any significant hits. Phylogenetic analysis of the
amino acid sequences of AD and ADL (Figure 1) shows that
trypanosomatids have developed two copies of AD, after their
divergence from other eukaryotes. Willert et. al.,  have
suggested that the most likely reason for the presence of two
copies of AD in trypanosoma lies in the regulation of production of
polyamines in a dynamic way, by regulating the expression level of
ADL under different environmental conditions. L. donovani being a
member of the same kinetoplastid family, might also have evolved
these two copies for the same reason. Leishmania ADLs have
developed at a later stage as compared to ADs. Analysis also
suggests that the L. donovani ADL is evolutionarily more distant
from the human AD than L. donovani AD.
Multiple sequence alignment of ADs from human, Leishmania
spp. and Trypanosoma spp. along with ADLs from L. donovani, L. major
L. infantum L. brazilensis, T. brucei and T. cruzi was done to identify
conserved & functionally important residues (Figure 2). The
alignment shows that most of the functionally important residues
are found to be identical between the human and trypanosomatids
ADs while the trypanosomatid ADLs have significantly different
residues (Figure 2). Glu 67 and Ser 68, residues essential for
autocatalysis in human AD  are also conserved in
trypanosomatids ADs which too undergoes autocatalysis [9,22]. In the
case of trypanosomatids ADLs including L. donovani, these residues
are not conserved, suggesting the absence of autocatalysis reaction,
as seen in T. brucei ADL. The absence of autocatalysis suggests that
ADL from trypanosomatids should not be annotated as
proenzyme in the gene database. As autocatalysis is an essential step of
decarboxylation mechanism, it also suggests that the
trypanosomatids ADLs are probably not capable of SAM decarboxylation
Structure-based sequence analysis of the SAM and putrescine
bound crystal structure of human AD (PDB ID 1I7B)  shows
that the residues involved in SAM positioning and binding i.e.,
Phe7, Leu65, Glu67, Phe223, Glu247 are conserved in L. donovani
AD (Phe32, Leu87, Glu89, Phe248, Glu271 respectively), and
interestingly, none of these residues are conserved in L. donovani
ADL. In fact, a majority of them are chemically different in L.
donovani ADL- Phenylalanines 7 and 223 correspond to Asp 15 and
192 in ADL, the stretch of residues corresponding to human Glu
247 is deleted in and at position 65, L. donovani ADL has a
methionine instead of a leucine. Residues involved in putrescine
binding, though are partially conserved in L. donovani ADL as well.
In summary, the residues involved in autocatalysis and SAM
positioning and binding are entirely different which suggests that
the L. donovani ADL might function in a novel manner. To further
explore and understand the role of L. donovani ADL, the protein
was cloned, over-expressed, purified and structurally and
Cloning and purification of L. donovani ADL
The L. donovani ADL gene was cloned, over-expressed and
purified using IMAC and was observed on SDS-PAGE as a single
band corresponding to 33 kDa, indicating the absence of any
autocatalytic cleavage reaction (Figure 3A), consistent with the
sequence alignment result (Figure 2). L. donovani ADL after IMAC
purification was found to undergo irreversible precipitation even
after dialysis and the rate of precipitation was directly proportional
to the protein concentration. Incorporation of putrescine (1
5 mM) in the buffer at every step of purification or keeping protein
concentration below 0.2 mg/ml decreased the precipitation,
suggesting the stabilizing effect of putrescine.
Biophysical characterization of L. donovani ADL
Size exclusion chromatography profile of L. donovani ADL shows
that it elutes at 10.4 ml on the SuperdexTM 75 10/300 column,
corresponding to ,66 kDa, suggesting L. donovani ADL is a dimer
(Figure 3B). The dimer was further confirmed by native PAGE
(Figure 3C) and is consistent with other trypanosomatid and
human ADs. However, it does not show any aggregation, unlike T.
brucei ADL which partially aggregates in the absence of AD .
Limited proteolysis experiment with trypsin failed to show any
additional bands in spite of the sequence having 25 Lys and Arg
residues, suggesting that the whole protein adopts a single folded
structure (Figure 3D) with the positively charged residues
presumably present in the interior of the protein.
Primary sequence analysis of ADL shows three tryptophans at
positions 4, 107 and 119. The fluorescence emission maxima of
tryptophan are seen at 341 nm (Figure 4A). This indicates that
these tryptophans are partially accessible to solvent. CD spectra
(Figure 4B), shows that ADL has sufficient secondary structure
elements 31% a-helix, 22% b-sheet, 47% random coil, as
calculated using the K2D3 server (http://www.ogic.ca/projects/
k2d3/) and is in agreement with the secondary structure
compositions predicted by the PHD server (http://npsapbil.ibcp.
fr) (Table 1).
Stability analysis of L. donovani ADL as a function of
temperature and pH
Since Leishmania has a digenetic lifecycle alternating between a
promastigote stage in sandfly and an amastigote stage present in
human macrophage between which it faces a variation in
temperature (25uC in sand fly and 37uC in human macrophage),
we analyzed the stability of L. donovani ADL over a range of
temperature. The thermal denaturation studies show L. donovani
ADL is stable up to 53uC, beyond which it begins to unfold. The
Tm of protein was found to be ,70uC and shows a sigmoidal
curve of unfolding (Figure 4C), suggesting cooperative
denaturation between native and denatured protein. Denaturation of this
protein is a single-step process in which the protein undergoes a
single transition from the native state to the denatured state. L.
donovani ADL shows maximum stability at pH 7.0 (Figure 4D) and
is sensitive to pH changes, resulting in heavy precipitation when
pH is varied by 1.5. Unfolding studies with ANS shows that both
urea and GdmCl denature through an intermediate species (figure
HYPERLINK slot:sensitivity towards pH change as it ishows
heavy precipitation even on 1.5 unit pH variation from
biologicalchanges from the biologica l pH. The protein shows
maximum stability at pH 7.0 which, corresponds to its biological
pH. The protein shows maximum stability at biological pH
(Figure 4D). Unfolding studies with ANS shows that both urea and
GdmCl denatured the L. donovani ADL through an intermediate
species (Figure S1, S2).
Figure 3. Over-expression, purification, size exclusion chromatography and trypsin digestion of of L. donovani ADL. (A) 12% SDS
PAGE of the purified L. donovani ADL. M-unstained protein marker; lane 1-unduced; lane 2-induced lane 3-load; lane 4-flow through; lane
5equilibration; lane 6-wash; lane 7-elution of L. donovani ADL showing single band after metal affinity chromatography. (B) Size exclusion
chromatography profile of L. donovani ADL showing protein elution at 10.4 ml on a Superdex 75 column, corresponding to 66 kDa molecular weight
i.e. dimer. (C) Confirmation of the dimer by Native Polyacrylamide Gel Electrophoresis. (D) Trypsin assisted limited proteolysis analysis of L. donovani
ADL at different time intervals showing that trypsin has no effect on L. donovani ADL.
Figure 4. Conformation profiles of ADL as analysed by fluorescence and far-UV CD spectroscopy. (A) Intrinsic tryptophan fluorescence
profile of L. donovani ADL shows emission maxima at 341 nm, indicating tryptophans are partially exposed. (B) Far-UV CD spectra (260 nm-200 nm)
of L. donovani ADL protein shows ADL is comprised of mixture of a-helix and b-sheet. (C) Thermal denaturation curve (h222) of L. donovani ADL
showing co-operative unfolding with midpoint at ,70uC. (D) Far-UV CD spectra of L. donovani ADL at pH range (49) showing maximum stability
near to biological pH (7.0).
Substrate binding analysis of L. donovani ADL
Despite lacking the essential Glu and Ser residues, T. brucei ADL
has shown a significant effect on the catalytic activity of AD by
playing an essential regulatory role [26,27]. L. donovani ADL also
lacks these residues and is possibly not involved in SAM
decarboxylation. In order to determine whether L. donovani ADL
binds with substrate while regulating the activity of AD as its T.
brucei homolog, we examined its substrate binding capacity, using
far-UV CD spectrum and tryptophan fluorescence. Tryptophan
fluorescence with increasing concentrations of SAM shows
quenching of the tryptophan emission maxima, suggesting SAM
binding to the protein. A saturation isotherm was plotted for SAM
and the binding of the ADL to SAM was identified by calculating
the DFmax and Kd values from a fit saturation isotherm equation
(Figure 5A and 5B), the DFmax and Kd values were found to be
194.5 and 5165 mM. Far-UV CD spectrum suggests that
increasing concentration of SAM induces a rearrangement of
secondary structure causing a conformational change (Figure 5C
and 5D). Taken together, the far-UV CD spectra and tryptophan
fluorescence conclusively shows that L. donovani ADL binds SAM.
To probe the effect of SAM on the structural organization of L.
donovani ADL, a limited proteolysis experiment with trypsin was
setup with SAM (080) mM. However, no digestion was seen
(Figure 5E) indicating that SAM does not expose any trypsin
Figure 5. SAM binding analysis by fluorescence and far-UV CD spectroscopy. (A) Graph shows effect of increasing concentration of SAM
causes quenching of tryptophan fluorescence (B) Saturation binding isotherm with dissociation constant 51 mM shows L. donovani ADL binds to SAM.
(C) Far-UV CD spectra shows change in secondary structure with increasing concentration of SAM. (D) Change in secondary structure, with increasing
concentration of SAM (0200 mM) was monitored by molar ellipticity value at h222, shows increasing concentration of SAM brings conformational
change in protein. (E) Trypsin assisted limited proteolysis in presence of increasing concentration of SAM (1080 mM) shows SAM binding does not
affects folding pattern.
Apart from SAM, putrescine also plays an essential role in the
stability of L. donovani ADL, with the protein precipitation
significantly reduced in a buffer containing putrescine during
purification. Further, putrescine is also found in crystal structures
of ADs from other organisms even when not being an explicit part
of the buffer, indicating that AD actively binds putrescine . It
was reported in T. cruzi that the AD-ADL heterodimer complex
needs putrescine for optimum activity while the corresponding T.
brucei heterodimer complex is self sufficient to stimulate maximum
activity and this difference has been correlated to their respective
environments [26,27]. However, the mechanism of putrescine
stimulation and interaction in T. cruzi is still unknown. In
Leishmania both promastigote and amastigote forms are capable
of absorbing putrescine from the environment [51,52]. In this
context we analyzed the putrescine binding property of L. donovani
ADL. Fluorescence spectroscopy shows quenching of tryptophan
fluorescence in a non-interpretable manner with increasing
concentration of putrescine which might be due to putrescine
binding to multiple sites. The presence of multiple putrescine
binding sites has also been reported earlier by Stanley et al., 1994
. Alternatively, putrescine being a cationic polyamine of small
size, its electrostatic interactions with other charged amino acids
surrounding tryptophan residues may also interfere with the
tryptophan fluorescence (Figure 6A). The secondary structure
content of L. donovani ADL show changes with increasing
concentration of putrescine up to 50 mM (Figure 6B and 6C)
and then remains constant, suggesting that the ADL binds
putrescine as well. The observed change in secondary structure
Figure 7. Homology modeling and prediction of SAM binding site. (A) Cartoon representation of the homology model of L. donovani ADL
(cyan), superimposed on to the crystal structure of human AD (pink). Ligands observed in the human structure, SAMe (red) and putrescine (red) are
also shown, as are the docked SAM and putrescine (yellow) to L. donovani ADL. Figure prepared with the help of Chimera 1.6.1. (B) Surface
representation of the L. donovani ADL monomer showing the five binding pockets of SAM as predicted by Q-site prediction server. The different
pockets are colored red, yellow, green, magenta and blue. The active site where SAM docked successfully is shown in inset (red). Figures are
generated with the aid of Pymol molecular visualization tool .
L. donovani ADL Asp15
due to putrescine was less in comparison to SAM, probably due to
its smaller size. Although this result shows that L. donovani ADL
binds putrescine and get stabilized as observed in purification the
detailed role and mechanism of putrescine is still not deciphered
and requires further experimental work. In the absence of such,
one can only conjecture that putrescine might either stimulate
SAM binding activity of L. donovani ADL or bring conformational
change that help in heterodimer complex formation with L.
donovani AD. Increasing concentration of putrescine, like SAM,
also has no effect on folding pattern of the ADL as seen in case of
trypsin digestion in increasing concentration of putrescine
In far-UV CD thermal denaturation studies, it was also
observed that the presence of SAM and putrescine decreases the
Tm by 23uC as compared to the native protein (Figure 6E). It was
already shown that L. donovani ADL binding to SAM and
putrescine, resulting in conformational change in secondary
Figure 9. Surface representation of AD:ADL heterodimer, as obtained by ClusPro 2.0. Surface representation of the L. donovani AD-ADL
heterodimer complex with AD (yellow) and ADL (red). Both monomers and the residues involved in heterodimer complex formation are shown
below. The interaction is stabilized by salt bridges between Lys96, Arg124, Asp173, Lys206 and Arg216 of L. donovani AD with Asp253, Glu106, Arg21,
Asp25 and Asp25 of L. donovani ADL.
ClusPro 2 weighed score
To understand the structural rationale of protein ligand
interactions, attempts were made to crystallize the protein, both
in its apo form and with SAM and putrescine as ligands. Initial
exploratory crystallization screens with a protein concentration of
4 mg/ml using standard crystal screens resulted in most of the
drops showing heavy precipitation, with some drops precipitating
immediately. To avoid precipitation, the protein concentration
was lowered to 12 mg/ml and other parameters such as pH and
temperature varied, which too did not result in diffracting crystals.
In the absence of suitable crystals, computational model was
generated to provide structural insights into the ligand binding
aspects of L. donovani ADL. As mentioned earlier, PSI-BLAST did
not result in any significant hits against PDB, so PHYRE fold
search, was used for the identification of template with similar fold.
PHYRE identified the human crystal structure, apo as well as in
complex with ligand as having a similar fold with 100%
confidence. The human AD (PDB ID 1MSV) which had the
minimum E value was used as the template for homology
modeling using Modeller 9.10 . The homology models of ADs
and ADLs of other Leishmania spp. and Trypanosoma spp were also
generated using similar protocol. The output models were
validated using standard tools and the models having minimum
internal energy, with 92.7% residues in the favored region of the
Ramachandran plot and an r.m.s.d value less than 2 A was
selected for further rationalization of protein ligand interaction
and protein-protein interaction studies
The L. donovani ADL model is representative of the core
architecture of proteins belonging to the SAM-decarboxylase
superfamily, consisting of four layer abba sandwich architecture
with the b-sheets comprising of seven and eight b-strands arranged
in antiparallel fashion (Figure 7A; Figure S3). This arrangement is
slightly different from the human AD where each b-sheet
comprises of eight strands. This is most likely due to L. donovani
ADL having lesser number of residues as compared to human AD.
The three tryptophan residues present in L. donovani ADL
sequence are found partially exposed within the homology model,
consistent with the intrinsic tryptophan fluorescence studies. The
secondary structure composition of homology model is analogous
to the predicted secondary structure composition with the proteins
belonging to SAM decarboxylase superfamily and is consistent
with the results obtained from far-UV CD spectroscopic studies.
Active site architecture of L. donovani ADL
(i) SAM binding. Having seen that L. donovani ADL binds
SAM and putrescine, we tried to locate the binding sites from the
homology model. However, multiple sequence alignment (Figure 2)
was not able to provide any relevant information regarding the
active site architecture of L. donovani ADL, as most of the functional
residues are different in L. donovani ADL. So, in order to probe the
active site architecture we used the Q-site finder server for active
site prediction. Q-site finder gave five probable binding pockets for
SAM (colored differently in Figure 7B) and these were taken as the
starting grids for docking the ligand using AUTODOCK 3.0.
However, in four of these sites SAM could not be docked
favorably. The energetically favorable (docking energy
210.79 kcal/mol) binding pocket for SAM, confirmed by
docking, shown in red color in inset (Figure 7B), was considered
for further analysis. Comparison of the SAM binding with human
AD crystal structure  showed significant differences (Figure 8A
and Table 2). In the human AD, SAM lies at the edge of the
bsheet interface, interacting with the residues belonging to both
sheets while in L. donovani ADL, the docked SAM lies near one
bsheet with its adenine ring in the b interface and the methionine
tail extending to the a-b interface. This difference is most likely
caused by the shorter length of b-strand (Leu60-Met65 in L.
donovani ADL and Gln60-Ser66 in human AD) which is involved in
interaction with the SAM in human AD. Closer examination of
the L. donovani ADL docked with SAM with the crystal structure of
human AD reveals the differences in the ligand binding (Table 2).
Glu67 and Glu247 are involved in binding SAM in human AD
while in L. donovani ADL, SAM interacts with only one similar
residue Glu64 with additional interactions from Gln52, Phe198
Comparative analysis also shows that in L. donovani ADL, the
adenine ring of SAM is stabilized by only one hydrogen bond,
through the interaction of its amino group with the a-carboxyl
oxygen of Gln52 which is different from human AD . L.
donovani ADL does not have any interaction with ribose sugar
unlike human AD. However, this is adequately compensated by
the carboxylic tail of SAM methionine being stabilized by the
aamino group of Phe198 and the amide nitrogen of His199. The
terminal amino group of SAM is stabilized by H-bond interaction
with nitrogen of His199 imidazole ring and oxygen atom of side
chain carboxylate of Glu64 (Figure 8A; Table 2).
As can be seen, the residues involved in SAM binding are
completely different from the human AD. Multiple sequence
alignment based comparison of residues involved in SAM binding
in L. donovani ADL with ADLs and ADs of trypanosomatids and
human AD shows that the residues found to be involved in SAM
binding with L. donovani ADL are conserved in Leishmania ADLs
but are different even from ADL of Trypanosoma spp., ADs of all
trypanosomatids and human AD which indicates the probability of
novel mode of mechanism of group of ADLs in Leishmania spp.
(ii) Putrescine binding site. The putrescine binding site of
AD from known organisms were studied in order to know the
residues which are involved in putrescine binding in case of L.
donovani ADL. This site is comprised of adjacently located
negatively charged residues. The homology model of L. donovani
ADL was screened for such sites and docking was done by
including glutamate residues with negatively charged
microenvironment in the grid. Four putrescine binding sites were
observed in the model of L. donovani ADL with docking energy.
25.30 to 26.36 consistent with the experimental observation of
putrescine binding to multiple sites. On comparison of the docked
putrescine-ADL with the corresponding human AD crystal
structure (PDB ID 1I7B) , one of the four binding site was
found to be identical to one putrescine binding site of human AD
(Figure 8B). Comparison of other putrescine binding site shows
that the docked putrescine adopts a different position in L. donovani
ADL, due to the short length of b-strand and completely different
orientation of proceeding loop as compared to the human AD.
The putrescine binding site of human AD interacts with the
residues from both b-sheets while in L. donovani ADL putrescine is
closer to one b-sheet and interacts with the residues on this sheet
only. The putrescine binding pocket of L. donovani is comprised of
similar Glu and Asp residues as found in the putrescine bound
crystal structure of human AD, the only difference being the
presence of Leu in place of Thr (Table 3). The other three
putresceine binding sites, obtained in L. donovani ADL by docking
studies also comprised of similar residues.
Binding residues analysis of SAM and putrescine shows that
SAM binding site of L. donovani ADL is sufficiently different from L.
donovani and human AD. However, in case of putrescine, binding
pattern and sequence alignment shows that binding residues are
similar in L. donovani ADL and human AD. Based on the SAM and
putrescine binding studies of L. donovani ADL, it can be
concluded the mode of SAM binding is probably the major
difference with human AD that needs to be exploited in any novel
Interaction analysis of ADL from Leishmania spp.
As AD and ADL in Trypanosoma have been shown to interact
together to form the catalytically active heterodimer complex,
wesought to see if this heterodimer formation is possible in
Leishmania as well. We took recourse to computational methods,
employing the STRING 9.0 and ClusPro 2.0 softwares for this
purpose. The interaction studies of homology models of ADL,
from members of trypanosomatids superfamily, with their
corresponding AD shows interaction, according to STRING 9.0.
Further, as a negative control, a pair of non-interacting proteins, L.
donovani nucleotide diphosphatase kinase b and
gamma-glutamylcysteine synthetase were input to the STRING 9.0 and no
interaction was observed (Data not shown). Further, ClusPro 2.0
and GRAMM-X shows positive docking result for L. donovani as
well as T. brucei AD-ADL pair. From these results, it is reasonable
to expect that these two proteins do interact as a heterodimer for
its function, as in Trypanosoma. Analysis of the docked structures
shows that the interaction is stabilized by salt bridges between
Lys96, Arg124, Asp173, Lys206 and Arg216 of AD with Asp253,
Glu106, Arg21, Asp25 and Asp25 of L. donovani ADL (Figure 9).
All interacting residues in the two proteins along with their
interaction are shown in Figure 9 and the interaction score of all
the servers are summarized in Table 4. These computational
results strongly indicate that AD and ADL do have the potential to
form a heterodimer, as in trypanosoma. We have recently cloned,
overexpressed and purified L. donovani AD (data not shown).
Preliminary interaction analysis using pull-down assays suggest
that t that L. donovani AD indeed form a heterodimer complex
with ADL (Figure S4). Encouraged with this result, further
characterization of the complex has also been initiated..
Trypanosomatids including L. donovani have two copies of the
protein belonging to the S-adenosylmethionine decarboxylase
superfamily, annotated here as AD and ADL. While AD from
different sources has been structurally and functionally
characterized, not much is known about ADL, although in Trypanosoma it
plays an essential role. To better understand this protein, we have
cloned expressed and purified L. donovani ADL in its native
conformation. L. donovani ADL is stable even in the absence of L.
donovani AD, unlike Trypanosoma where ADL shows partial
aggregation in absence of AD. We carried out its biochemical,
biophysical and computational characterization to analyze its
structural and functional properties. Based on this study, L.
donovani ADL is a member of group comprising novel proteins of
Sadenosylmethionine decarboxylase superfamily i.e, ADLs, sharing
some key features of this superfamily such as having similar
secondary structural components, tertiary structure and a dimeric
quaternary association of native protein. Besides these common
features, leishmanial ADL also exhibits several distinct features
from human AD and even from ADs of trypanosomatids. It has no
significant sequence identity with the other members of the SAM
decarboxylase superfamily, does not undergo autoprocessing
reaction and should therefore not be annotated as proenzyme.
Interestingly, our study has also shown that L. donovani ADL binds
to SAM and putrescine, natural substrates of AD. To rationalize
the ligand binding, computational homology modeling was
undertaken followed by docking of these ligands. Homology
modeling reveals that the tertiary structure exhibits the classical
abba sandwich arrangement albeit with a subtle difference.
Instead of the predominant arrangement of 8 b-strands in each
bsheet, L. donovani ADL appears to have a 7-stranded and an
8stranded sheet. Docking studies confirmed that ADL could bind
SAM and putrescine. On comparison with the crystal structure of
human AD, the SAM binding residues are distinctly different. L.
donovani ADL is also involved in interaction with AD favoring
heterodimer complex formation as in Trypanosoma. The fact that
ADL binds to SAM and putrescine suggests that the functioning of
the AD-ADL heterodimer might be significantly different from
Trypanosoma. Two possible mechanisms are plausible: Both AD and
ADL can be equally active during catalysis and it may be that
ADL might still play only a limited regulatory role and the actual
mechanism needs to be delineated experimentally. In either case,
it can be said that ADL, as compared to AD, appears to be a better
candidate as a potential drug target. However, further
characterization and validation of this complex is necessary. To this end, we
have initiated purification of L. donovani AD as well and
preliminary results suggest that L. donovani AD indeed form a
heterodimer complex with ADL. Further analysis of stability of
this heterodimer complex is in progress.
Figure S1 Cartoon representation of homology model of
monomeric L. donovani ADL (cyan), superimposed with
structure of human AD (pink), shows that L. donovani
ADL also have same structural organization abba as in
case of human AD, but ADL has one b-strand missing
due to short length as shown in figure. Figure is made with
the help of Chimera 1.6.1.
Figure S2 Unfolding studies of ADL in presence of urea.
The changes in tertiary structure were monitored by fluorescence
studies using tryptophan as intrinsic fluorophore and ANS as
extrinsic fluorophore. (AB) Effect of increasing concentration of
urea on tryptophan fluorescence was monitored at tryptophan
emission maxima 341 nm, shows increasing concentration of urea
causes gradual red shift of ADL due to unfolding of protein with
complete unfolding at 6 M urea. (CD) ANS fluorescence
emission spectra with increasing concentration of urea, monitored
at 465 nm. Graph shows emission maxima increases with increase
in concentration of urea up to 0.5 M urea, then gradually
decreased with minima at 6 M urea, due to loss of hydrophobic
Figure S3 Unfolding studies of L. donovani ADL in
presence of GdmCl. The changes in tertiary structure were
monitored by fluorescence studies using tryptophan as intrinsic
fluorophore and ANS as extrinsic fluorophore. (AB) Effect of
GdmCl on tryptophan fluorescence of L. donovani ADL monitored
at 341 nm emission maxima. Graph shows increased
concentration of GdmCl causes unfolding of protein with maximum
transition at 1.5 M GdmCl and protein gets fully exposed at
2 M concentration. (CD) ANS fluorescence emission spectra with
increasing concentration of GdmCl monitored at 465 nm shows
emission maxima increases with increasing concentration of
GdmCl up to 0.5 M GdmCl, and then gradually decreased to a
minimum value at 4 M GdmCl.
Figure S4 AD-ADL interaction observed from GST pull
down assay. The cell lysate containing AD-GST construct (in
Tris-HCl pH 7.5 and 150 mM NaCL) was incubated with
glutathione agarose for two hours and the unbound cell lysate
discarded and washed with buffer containing Tris-HCl pH 7.5and
1M NaCl, before incubating with cell lysate containing
66HisADL for 2 hours, washed with 5 column volumes of the same
buffer and eluted with reduced glutathione. A similar experiment
using GST alone instead of AD-GST was also performed as
control. The elution products were analyzed on 12% SDS PAGE
(top panel): Lane 1 marker, Lane 2 elution of GST with ADL,
Lane 3: elution of AD-GST with ADL and Lane 4: AD alone. The
band at ,60 kDa corresponds to full length AD-GST while the
band at ,35 kDa corresponds to the autocatalyzed N-terminal
fragment of AD (9 kDa) fused to 26 kDa GST (Mr 35 kDa) as well
as ADL (Mr 33 kDa). To resolve this, the eluted products were
then probed with anti-GST (middle panel) and anti-His (bottom
panel) antibodies which show the presence of the two species. The
absence of a band corresponding to ADL in Lane 2 in the anti-His
blot confirms specific AD: ADL interaction.
We acknowledge the Institute of Microbial Technology, Chandigarh,
INDIA and the Advanced Instrumentation Research Facility, Jawaharlal
Nehru University, New Delhi, INDIA for providing facility for far-UV CD
experiment. This manuscript bears the CDRI communication No. 8455.
Conceived and designed the experiments: SPS PA JVP. Performed the
experiments: SPS PA. Analyzed the data: SPS PA JVP. Contributed
reagents/materials/analysis tools: JVP. Wrote the paper: SPS PA JVP.
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