Crystal Structures of TbCatB and Rhodesain, Potential Chemotherapeutic Targets and Major Cysteine Proteases of Trypanosoma brucei

Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America.
PLoS Neglected Tropical Diseases (Impact Factor: 4.45). 06/2010; 4(6):e701. DOI: 10.1371/journal.pntd.0000701
Source: PubMed
Trypanosoma brucei is the etiological agent of Human African Trypanosomiasis, an endemic parasitic disease of sub-Saharan Africa. TbCatB and rhodesain are the sole Clan CA papain-like cysteine proteases produced by the parasite during infection of the mammalian host and are implicated in the progression of disease. Of considerable interest is the exploration of these two enzymes as targets for cysteine protease inhibitors that are effective against T. brucei.
We have determined, by X-ray crystallography, the first reported structure of TbCatB in complex with the cathepsin B selective inhibitor CA074. In addition we report the structure of rhodesain in complex with the vinyl-sulfone K11002.
The mature domain of our TbCat*CA074 structure contains unique features for a cathepsin B-like enzyme including an elongated N-terminus extending 16 residues past the predicted maturation cleavage site. N-terminal Edman sequencing reveals an even longer extension than is observed amongst the ordered portions of the crystal structure. The TbCat*CA074 structure confirms that the occluding loop, which is an essential part of the substrate-binding site, creates a larger prime side pocket in the active site cleft than is found in mammalian cathepsin B-small molecule structures. Our data further highlight enhanced flexibility in the occluding loop main chain and structural deviations from mammalian cathepsin B enzymes that may affect activity and inhibitor design. Comparisons with the rhodesain*K11002 structure highlight key differences that may impact the design of cysteine protease inhibitors as anti-trypanosomal drugs.


Available from: Zachary B Mackey
Crystal Structures of TbCatB and Rhodesain, Potential
Chemotherapeutic Targets and Major Cysteine Proteases
Trypanosoma brucei
Iain D. Kerr
, Peng Wu
, Rachael Marion-Tsukamaki
, Zachary B. Mackey
, Linda S. Brinen
1 Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America, 2 Department of
Pathology and the Sandler Center for Basic Research in Parasitic Diseases, University of California San Francisco, San Francisco, California, United States of America
Trypanosoma brucei is the etiological agent of Human African Trypanosomiasis, an endemic parasitic disease
of sub-Saharan Africa. TbCatB and rhodesain are the sole Clan CA papain-like cysteine proteases produced by the parasite
during infection of the mammalian host and are implicated in the progression of disease. Of considerable interest is the
exploration of these two enzymes as targets for cysteine protease inhibitors that are effective against T. brucei.
Methods and Findings:
We have determined, by X-ray crystallography, the first reported structure of TbCatB in complex
with the cathepsin B selective inhibitor CA074. In addition we report the structure of rhodesain in complex with the vinyl-
sulfone K11002.
The mature domain of our TbCatNCA074 structure contains unique features for a cathepsin B-like enzyme
including an elongated N-terminus extending 16 residues past the predicted maturation cleavage site. N-terminal Edman
sequencing reveals an even longer extension than is observed amongst the ordered portions of the crystal structure. The
TbCatNCA074 structure confirms that the occluding loop, which is an essential part of the substrate-binding site, creates a
larger prime side pocket in the active site cleft than is found in mammalian cathepsin B-small molecule structures. Our data
further highlight enhanced flexibility in the occluding loop main chain and structural deviations from mammalian cathepsin
B enzymes that may affect activity and inhibitor design. Comparisons with the rhodesainNK11002 structure highlight key
differences that may impact the design of cysteine protease inhibitors as anti-trypanosomal drugs.
Citation: Kerr ID, Wu P, Marion-Tsukamaki R, Mackey ZB, Brinen LS (2010) Crystal Structures of TbCatB and Rhodesain, Potential Chemotherapeutic Targets and
Major Cysteine Proteases of Trypanosoma brucei. PLoS Negl Trop Dis 4(6): e701. doi:10.1371/journal.pntd.0000701
Editor: Christian Tschudi, Yale School of Public Health, United States of America
Received December 18, 2009; Accepted April 8, 2010; Published June 8, 2010
Copyright: ß 2010 Kerr et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: Portions of this work were supported by National Institutes of Health award AI35707 and the Sandler Foundation. 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.
* E-mail:
. These authors contributed equally to this work.
¤ Current address: Department of Cell Biology and Physiology, School of Medicine, Washington University, St. Louis, Missouri, United States of America
The protozoan parasite Trypanosoma brucei is the cause of Human
African Trypanosomiasis (HAT, sleeping sickness) in humans and
nagana in domestic livestock [1,2,3]. With over 60 million people
at risk and 50,000–70,000 infected, new drugs are required to
control the spread of disease and associated mortality. Only four
drugs are approved for treatment [4], however, most are limited
by parasite resistance [4] and marked host toxicity [5,6,7,8]. A
new combination therapy for treating HAT has been approved
recently by the World Health Organization (WHO), however no
newly developed drugs are on the horizon [9,10]
Clan CA cysteine proteases play central roles during the lifecycle of
many parasitic organisms [11] and have been established as effective
drug targets in treating many parasitic diseases [12,13,14,15].
Bloodstream T. brucei parasites express two papain family cysteine
proteases, rhodesain (brucipain, trypanopain), a cathepsin L-like
enzyme and TbCatB, a cathepsin B-like enzyme. Rhodesain is the
more abundant of the two cathepsins and is required to cross the
blood-brain barrier [16]. RNA interference of TbCatB is able to
rescue mice from a lethal T. brucei infection [16]. RNAi knockdown of
rhodesain, however, only prolongs mouse survival [17]. TbCatB may
protease inhibitors targeting T. brucei infection. A cysteine protease
inhibitor, Z-Phe-Ala-CHN2, has been shown to be lethal to T. brucei
both in vitro and in vivo [18,19] and our efforts are focused on
elucidating key features of inhibitors that will optimize both specificity
and potency.
Both cathepsin B-like and cathepsin L-like proteases share the
common features of Clan CA cysteine proteases, including a
conserved catalytic triad (Cys/His/Asn) and a substrate-binding
site comprised of many structurally conserved residues [20]. One
major difference between cathepsin L and cathepsin B enzymes is
the presence of an ‘occluding loop’ of approximately 20 amino
acids located on the surface of cathepsin Bs that confers an
additional exopeptidase activity to these cysteine proteases [21]. 1 June 2010 | Volume 4 | Issue 6 | e701
Page 1
To elaborate on the structural and biochemical differences
between cathepsin L and cathepsin B-like cysteine proteases in T.
brucei, and to aid in the design of better inhibitors, we have
determined the high-resolution crystal structures of rhode-
sainNK11002 and the first crystal structure of T. brucei cathepsin
B, TbCatBNCA074.
Materials and Methods
Production of the TbCatB N-glycosylation mutant
Recombinant TbCatB was modified from a previously de-
scribed protocol [22]. The gene encoding the full-length zymogen
(minus the N-terminal signal sequence) was sub-cloned from a
pPICZaB-TbCatB construct into the pPICZaA expression vector
(Invitrogen). Site-directed mutagenesis using the QuickChange
system (Stratagene) was used to add a C-terminal His tag and to
incorporate an N216D mutation (full-length numbering) at a
predicted glycosylation site. The expression of a glycoslylation site
mutant in P. pastoris is a strategy that has recently been successful
in our structural studies of the homologous parasite cysteine
protease cruzain [23,24].
Expression and purification of TbCatB
Pichia pastoris strain 633 was transformed with 20mg of BstXI
linearized TbCatB-N216D according to the manufacturer’s
instructions (Invitrogen). A single transformed colony was used
to inoculate 2–3 ml of YPD-zeocin media and the culture was
grown overnight at 30uC. The following day, 2 liters of YPD-
zeocin media were inoculated with the starter culture and
incubated at 30uC, with constant shaking at 250rpm, until cell
density reached an OD
of 3–4 (typically 2–3 days). Cells were
harvested at 1500g for 15min and the pellet was rinsed with 100ml
BMM media and centrifuged at 1500g for 15min to remove
residual YPD media. Cells were then harvested and resuspended
in BMM media to an OD
of approximately 1.0. Induction of
protein overexpression was carried out in a BioFlo110 Fermentor/
Bioreactor (New Brunswick Scientific) with the addition of 1%
methanol, twice a day. Supernatant was collected after 3 days
incubation and concentrated to 50ml using an Ultrasette
tangential flow device with a 30kDa cut-off (Pall Corporation).
The concentrated sample was adjusted to a final concentration of
300mM NaCl and 10mM Imidazole and incubated with 2ml of
Ni-NTA beads (Qiagen) overnight at 4uC. The beads with the
bound sample were transferred to an empty PD-10 column (GE
Healthcare), rinsed with 100mM phosphate pH 6.0, 300mM
NaCl, 10mM Imidazole, and eluted with 100mM phosphate
pH 6.0, 300mM NaCl and 200mM Imidazole. Eluted proteins
were dialyzed against 1L buffer containing 20mM Tris-HCl
pH 8.0, 1mM EDTA and 5mM b-mercaptoethanol. Dialysis
buffer was changed after 2 hours and continued overnight at 4uC.
Activation, inhibition and purification of TbCatB
To produce the mature form of the protease, purified enzyme
was auto-activated in a buffer containing 100mM sodium acetate
pH 4.5, 10mM DTT, 1mM EDTA, 100mM NaCl and 100ug/ml
dextran sulfate (MW 5000). Protease activity was monitored every
hour using Z-Phe-Arg-AMC as the substrate [22,25,26]. After
reaching its maximum, activity was completely abolished with the
addition of 10-fold molar excess CA-074 (Sigma-Aldrich). The
mixture was incubated overnight, with gentle stirring, to ensure
complete inhibition of the activated enzyme.
Inhibited enzyme was then dialyzed against 20mM Tris-HCl
pH8.0, 1mM EDTA and 5mM b-mercaptoethanol and applied to
a Mono-Q column (GE Healthcare) with TbCatBNCA074 eluting
at approximately 150mM NaCl (gradient 0–1M NaCl) at a flow
rate of 1ml/min. Fractions corresponding to the protease were
pooled and further purified on a Superdex 200 gel-filtration
column (GE Healthcare). The purified sample was concentrated to
3mg/ml and the buffer exchanged to 20mM Tris-HCl pH 8.0.
Edman sequencing of activated TbCatB
Three separate aliquots of TbCatB from the same batch were
activated, purified and inhibited with CA074 as described above.
mg of activated, inhibited protein was run on an SDS-PAGE
gel and transferred on to a PVDF membrane. The blot was run for
90mins hrs at a current of 125mA. The same experiment was
performed with a single purified, unactivated, sample of the
enzyme. Bands containing mature and full-length TbCatB were
excised from the membrane and sent for N-terminal Edman
sequencing at the Protein and Nucleic Acid Facility (PAN),
Stanford University Medical Center (
Western Blot analysis of recombinant and native TbCatB
T. brucei were cultured in HMI-9 medium to a density of
approximately 1.5610
tryps per/ml. To obtain crude extracts,
tryps were pelleted in 50 ml conical centrifuge tubes by
centrifugation at 2500 rpm. The medium was aspirated and the
pellet re-suspended in 250 of lysis buffer (50mM Sodium Acetate
pH 5.5, 1mM EDTA, 1% Tx-100). The lysate was clarified by
centrifugation and the protein concentration of the supernatant
was measured by Bradford assay (Bio-Rad). Recombinant,
activated TbCatB was prepared and purified to the stage of anion
exchange chromatography (Mono Q), as above. The crude lysate
containing native TbCatB and the activated recombinant sample
were both prepared for analysis by adding 56 SDS loading buffer
and boiling for 2-minutes. 40
mg of the crude lysate or 0.3mgof
purified activate TbCatB was loaded into the well of a Novex 12-
well Bis-Tris mini gel (Invitrogen) and resolved by SDS-PAGE at
180 volt with constant current for 1.5 hours. The gel was
transferred onto a PVDF membrane (Bio-Rad) and blocked for
2 hours in buffer containing 3% milk and 0.5% BSA. After
blocking, the blots were incubated with rabbit anti-TbCatB
antiserum and diluted 1:1,000 overnight at 4uC. The blots were
washed 3 times for 5 minutes with TBST and then incubated at
room temperature for 1 hour with goat anti-rabbit serum (GE
Healthcare) diluted at 1:1,000 in TBS. Afterwards, the blots were
washed 3 times for 5 minutes with TBST and once with TBS. The
Author Summary
Proteases are ubiquitous in all forms of life and catalyze
the enzymatic degradation of proteins. These enzymes
regulate and coordinate a vast number of cellular
processes and are therefore essential to many organisms.
While serine proteases dominate in mammals, parasitic
organisms commonly rely on cysteine proteases of the
Clan CA family throughout their lifecycle. Clan CA cysteine
proteases are therefore regarded as promising targets for
the selective design of drugs to treat parasitic diseases,
such as Human African Trypanosomiasis caused by
Trypanosoma brucei. The genomes of kinetoplastids such
as Trypanosoma spp. and Leishmania spp. encode two Clan
CA C1 family cysteine proteases and in T. brucei these are
represented by rhodesain and TbCatB. We have deter-
mined three-dimensional structures of these two enzymes
as part of our ongoing efforts to synthesize more effective
anti-trypanosomal drugs.
Structural Analysis of TbCatB and Rhodesain 2 June 2010 | Volume 4 | Issue 6 | e701
Page 2
immunoblots were then analyzed by ECL reagent (GE Health-
care) (Figure S1).
Crystallization of recombinant TbCatBNCA074
Crystallization conditions were screened with a Mosquito drop-
setting system (TTP Labtech) against a number of commercially
available kits. Optimization of crystal conditions was performed
manually on the basis of initial screening hits. Hanging drops of 1–
ml were set up with 3mg/ml TbCatBNCA074, and 1M LiCl, 10%
PEG 3350, 0.2M Tris-HCl pH 7.6. Rod-shaped crystals formed
after 3 days and reached a maximum size after 5–10 days. Crystals
were flash-cooled in well solution supplemented with 30% glycerol
and mounted for the Stanford Auto Mounter (SAM) system [27].
Crystallization of recombinant rhodesainNK11002
Rhodesain was expressed in P. pastoris and purified and
activated as described previously [25,26,28] with a Ser172Ala
mutation incorporated to remove an N-glycosylation site from the
mature domain of rhodesain. Active rhodesain was incubated with
a 10-fold molar excess of the inhibitor K11002, dissolved in
DMSO. Complete inhibition of enzymatic activity was confirmed
by fluorometric assay against the substrate Z-Phe-Arg-Nmec
(Bachem). Purified rhodesain was concentrated to approximately
8 mg/ml in preparation for crystallization. Crystals of maximum
size were obtained after approximately 10 days via the sitting drop
method, from a precipitating solution of 1.6M ammonium sulfate,
0.1M Bicine pH 9.0 at 18uC. Crystals were flash-cooled in liquid
nitrogen in well solution supplemented with 20% ethylene glycol.
Structure determination of TbCatBNCA074 and
All diffraction data were collected at the Stanford Synchrotron
Radiation Lightsource (SSRL). RhodesainNK11002 data were
collected to 1.16A
on BL9-1 after selecting an optimal crystal from
screening performed with the robotic SAM system [27].
TbCatBNCA074 data were collected following a similar protocol
on SSRL BL7-1 with the best crystals diffracting to 1.6A resolution.
For both datasets, reflections were indexed and integrated in
MOSFLM [29] and scaled and merged in SCALA [30]. The
TbCatBNCA074 structure was solved by molecular replacement
using MOLREP [31] with a homology model built by MOD-
ELLER [32] from the ensemble coordinates of human cathepsin B
(1GMY), rat cathepsin B (1CTE) and cruzain (1F2A). Two clear
rotation function solutions were obtained in space group P2
peak heights/sigma of 13.27 and 12.91 respectively, corresponding
to two molecules in the asymmetric unit. The translation function
yielded a clear solution for the dimer with a score of 0.53 and initial
of 54.6%. The structure of rhodesainNK11002 was solved by
molecular replacement using PHASER [33] with a model derived
from a prior structure of rhodesain bound to a different vinyl sulfone
containing inhibitor (PDB ID 2P7U). A single, strong solution was
obtained in space group P2
with a rotation function Z-score of
19.3, a translation Z-score of 28.7 and an initial LLG (log likelihood
gain) of +896, which improved to +2022.7 with 6 cycles of rigid
body refinement.
Following rigid body and maximum likelihood restrained
refinement in REFMAC5 [34], the inhibitor molecules were
placed in clear mFo-DFc difference electron density in using
COOT [35]. During these initial stages of refinement the
occluding loop residues in TbCatB were removed from the model
and rebuilt as the difference density became clear. Both models
were completed through iterative rounds of manual model
building and refinement with COOT [35] and REFMAC5 [34].
TLS parameterization was used to refine the TbCatBNCA074
structure, while anisotropic temperature factors were refined in the
case of rhodesainNK11002. Water molecules were placed in each
structure with COOT and manually assessed. The final rhode-
sainNK11002 model contains 1 molecule of rhodesain, 1 inhibitor
molecule, 402 water molecules and 11 ethylene glycol molecules.
The final TbCatBNCA074 model contains 2 molecules of TbCatB,
2 inhibitor molecules, 572 water molecules, 6 glycerol molecules, 1
Tris molecule, a lithium ion and a magnesium ion. Statistics for
data collection and refinement are given in Table 1. The
coordinates and observed structure factors amplitudes for
rhodesainNK11002 and TbCatBNCA074 have been deposited in
the Protein Data Bank under accession codes 2P86 and 3HHI
Overall structures of rhodesainNK11002 and
The structure of rhodesainNK11002 was determined to 1.16A
resolution and refined to an R
of 13.0% and an R
of 11.0%
Table 1. X-ray data collection and refinement statistics.
Data Collection rhodesainNK11002 TbCatBNCA074
Resolution 1.16 (1.19-1.16) 1.60 (1.69-1.60)
Space Group P2
Unit cell parameters
a, b, c (A
) 33.66, 78.63, 80.73 53.88, 75.13, 75.90
a, b, c (u) 90.0, 90.0, 90.0 90.0, 105.0, 90.0
Total unique reflections 68633 74519
Completeness 91.9 (80.0) 96.9 (95.5)
Redundancy 7.1 (6.9) 9.5 (9.5)
0.043 (0.120) 0.093 (0.687)
I/s I 27.2 (14.9) 17.6 (4.8)
Wilson B-factor (A
) 6.1 15.1
Resolution range (A
) 40.36–1.16 73.32-1.60
(%) 13.0 17.8
(%) 11.0 14.7
Number of water molecules 447 572
Average B factor (A
protein 8.51 10.69
water 24.0 23.32
Rms deviations
Bond lengths (A
) 0.017 0.020
Bond angles (u) 1.88 1.72
Ramachandran plot
Residues in favored
regions (%)
95.9 96.7
Residues in allowed
regions (%)
99.1 100
Number of outliers 2 0
as defined by Molprobity [46].
Structural Analysis of TbCatB and Rhodesain 3 June 2010 | Volume 4 | Issue 6 | e701
Page 3
(Figure 1). The complex crystallized in spacegroup P2
one complete copy of the rhodesain mature catalytic domain
(residues 1–215) in the asymmetric unit. The amino acid residues
at the beginning of mature rhodesain structure are APAA,
consistent with the predicted cleavage site at the N-termini of
mature rhodesain, cruzain and other cathepsin L-like proteases.
We recently reported the first crystal structure of rhodesain in
complex with the vinyl sulfone inhibitor K11777 (PDB ID 2P7U)
[36]. Superimposition of this vinyl sulfone complex with the
K11002 complex reported here matches 214 a-carbons with root
mean square distances of 0.27A
. An interesting feature of the
K11002 complex is the observation of a dual conformation of the
phenylsulfone moiety at the P19 position of the inhibitor (Figure 2).
The optimal model to data agreement was obtained by refinement
of the two conformations as a 70%/30% combination of relative
occupancies. We have previously observed that this group can flip
out of the S19 pocket [36].
The TbCatBNCA074 complex crystallized in spacegroup P2
with two molecules in the asymmetric unit and was refined to
resolution to a final R
of 17.8% and R
of 14.7%
(Figure 1). Chains A and B comprise residues 78–335 and 78–337
of full-length TbCatB, respectively. With the predicted maturation
cleavage site of the enzyme between Pro93 and Leu94 [18], we
were surprised to observe that our crystal structure of the
activated, mature form of TbCatB contains an additional 16
residues at the N-terminus preceding the predicted site of
activation. In light of the non-standard start of the catalytic
domain, this structure is numbered from the N-terminal signal-
sequence, with methionine as residue 1. For clarification in the
text, TbCatB residues have the ‘standard’ mature domain
numbering, according to human cathepsin B, in superscript. In
the occluding loop of TbCatB (Pro189
) the electron
density is somewhat diffuse in parts and these more flexible regions
were therefore modeled at reduced occupancy. Interestingly, in
chain B (where the electron density for the occluding loop is clear)
we observed a dual conformation for the backbone carbonyl of
and the backbone amide of His195
. A nearby
electron density peak was modeled and refined as a water
molecule. Although there was no significant difference density
around this water when refined at full occupancy, we decided to
model this position at 50% occupancy (HOH565) to reflect its
transient interaction with the peptide chain in this region.
Refinement of this peak as a common cellular/buffer ion at full
occupancy (Li, Na, Mg
) yielded significant positive or
negative difference density.
N-terminal sequence analyses of TbCat
In light of the unexpected residues observed N-terminal to the
predicted maturation site, three separate aliquots of TbCatB were
analyzed by Edman sequencing to determine, under the activation
conditions described above, the full-length sequence of the mature
domain prior to crystallization. All three reactions yielded
LREAKRLNNV as the N-terminal peptide sequence. This
corresponds to a peptide 61 residues into the full-length TbCatB
sequence. The Asn at position 69 is Gly according to the published
sequence (Genbank accession code AAR88085) and we presume
this to simply be an experimental error due to the low amount of
sample used for the blot. Additional N-terminal sequencing studies
using E64 as the inhibitor and a larger quantity of sample confirm
this residue to be Gly69 (data not shown). To rule out an
activation event during cell culture and expression of the
recombinant enzyme in P. pastoris, we also sequenced a purified,
unactivated sample. This yielded the peptide EAEFALVAED; the
first four residues are a cloning artifact from the 59 end of the
expression vector. The remaining six residues correspond to the
expected beginning of the cloned sequence (minus the signal
sequence). The implications of these findings are discussed below.
To determine whether an unexpected activation event occurs
in-vivo, we compared the size, by Western Blot analysis, of our
recombinant, purified mature TbCatB with a sample of the native
protein present in crude T. brucei lysates (Figure S1). With the
predicted size of mature TbCatB calculated to be 26–27kDa, the
Figure 1. Structures of rhodesain and TbCatB. Stereo pairs of (A) rhodesain and (B) TbCatB. The figure is annotated with the secondary
structure and the L and R domains are colored green and grey respectively. The occluding loop and N-terminal extension in TbCatB are colored red.
Structural Analysis of TbCatB and Rhodesain 4 June 2010 | Volume 4 | Issue 6 | e701
Page 4
blot clearly shows that both recombinant and activated TbCatB
are larger than predicted, with the recombinant form being the
slightly larger of the two. While there are no modifications to
prevent glycosylation of the native form, we have previously
observed the size of the glycosylated and (Endo H-treated)
deglycosylated protein to be the same (data not shown).
We report the crystal structures of rhodesainNK11002 and
TbCatBNCA074, two papain family cysteine proteases implicated
in the pathogenesis of Trypanosoma brucei infection (Figure 1). The
structure of rhodesainNK11002 is similar to that of rhode-
sainNK11777 (PDB ID 2P7U) [36] with the bound inhibitor
varying only at the P3 position (N-methyl piperazine in K11777,
morpholino urea in K11002). While a number of hydrogen bonds
are formed between residues lining the substrate-binding site and
the inhibitor backbone, a number of hydrophobic residues also
provide binding energy, principally in the S2 subsite (Figure 2), the
subsite that confers selectivity for this class of enzyme. This is in
contrast with the TbCatBNCA074 complex where hydrogen
bonding between the enzyme and inhibitor dominate over
hydrophobic interactions. The phenylsulfone moiety at P19 is a
common motif represented in many parasite cysteine proteaseN
vinylsulfone complexes. The dual conformation of this moiety in
the rhodesainNK11002 structure is unique for a parasite cysteine
proteaseNvinylsulfone complex and we have not observed this in
other high resolution structures of rhodesain or the closely related
cruzain from Trypanosoma cruzi.
The TbCatB crystal structure, the first reported for this enzyme,
is similar in overall structure to homologous cathepsins B-like
enzymes studied (Table S1), with the majority of the variation
found in the occluding loop region (discussed below). Our crystal
structure also reveals several interesting features that are atypical
of a cathepsin B-like cysteine protease. Cathepsin B family
members were originally defined in vertebrate systems as
possessing an acidic residue at the bottom of the S2 subsite that
allows for the accommodation of basic residues in the pocket
[37,38]. TbCatB has a Gly at this position, which opens up the
pocket allowing larger P2 substituents to be targeted to this part of
the active site cleft (Figure 3). Homology modeling previously
indicated an acidic functionality around the S2 subsite of TbCatB
[39], that may be able to take advantage of a positive charge at the
P2 position of small molecule inhibitors. These acidic residues line
the sides (Asp166
, Asp168
, Asp258
) and bottom (Asp327
of the pocket. In our structure Asp258
and Asp327
available for binding and in each copy of TbCatB interact with a
glycerol molecule from the cryoprotectant solution (Figure 4).
Superimposition of TbCatBNCA074 and rhodesainNK11002
highlights structural differences that cause rhodesain to be more
sterically restricted at the S2 subsite (Figure 5). Firstly, Asp166
TbCatB is substituted for a Leu in rhodesain (Leu67); Asp166
TbCatB is able to pack itself against helix a3 where it establishes a
number of hydrogen bonding interactions (Figure 5a). Leu67
packs more favorably against the hydrophobic environment of the
rhodesain S2 subsite with the large hydrophobic phenylalanyl at
the P2 position of K11002. This residue therefore points in toward
the substrate-binding site in rhodesain. Secondly, rhodesain has
Figure 2. Inhibitor binding in TbCatB and rhodesain. Surface (left) and ball and stick (right) active site representations of (A) the
rhodesainNK11002 complex and (B) the TbCatBNCA074 complex. Inhibitor molecules are colored grey and the unbiased mFo-DFc electron density for
each is colored violet. Hydrophobic interactions with neutral/non-polar residues are mapped on the surface and colored purple.
Structural Analysis of TbCatB and Rhodesain 5 June 2010 | Volume 4 | Issue 6 | e701
Page 5
the larger Ala208 (Gly328
in TbCatB) at the bottom of the S2
subsite, making the pocket shallower (Figure 5b). Finally, the loop
between strands b2 and b3 in rhodesain is anchored to an adjacent
loop (between strands b5 and b6) by a disulfide bridge between
Cys155 and Cys203. A number of direct and water-mediated
hydrogen bonding interactions stabilize this conformation and
Gln159 and Leu160 are pulled into the S2 subsite to further
narrow the pocket (Figure 5c). In TbCatB, the b2–b3 loop lacks
the cysteine required to form the anchoring disulfide bridge, and is
glycine-rich (Gly269
, Gly276
, Gly280
and Gly281
when compared with rhodesain. The additional flexibility allows
the C-terminal portion of the TbCatB loop to adopt a
conformation similar to that found in human cathepsin B,
removed from the S2 subsite and oriented towards the prime
sites. Of note, the mobility of this loop was recently alluded to in
homology modeling studies by Mallari et al. in comparison with
human cathepsin L [40].
TbCatB has an ‘occluding loop’, a unique feature of cathepsin
B-like enzymes, which spans the prime side of the substrate
binding site and distinguishes them from the cathepsin L-like
enzymes [11,21]. In TbCatB, the loop is three residues longer than
in mammalian homologs and we note a dual peptide conformation
between His 194
and His195
. The occluding loop in TbCatB
further deviates from homologous structures between residues
. Human, rat and bovine cathepsin B have an
invariant ‘‘GEGD’’ motif in this region. The glycine residues
flanking Glu122 confer additional flexibility in this region such
that the negatively charged residue is able to flip in and out of the
active site [41] (Figure 3). The corresponding motif in TbCatB,
‘‘FNFD’’, lacks this flexibility and both Phe208
and Phe210
stack with the N-terminal residue (Phe189
) of the occluding
loop, creating a more stable opening around S19. This feature of
the TbCatB occluding loop presents the possibility to engineer
additional specificity into inhibitors targeting this enzyme. Indeed
Mallari et al. have shown that out of a series of 56 compounds, only
those with a specific N9 substituent (hydroxypropyl) were
reasonable human CatB inhibitors. The authors propose this
may be due to the ability of this substituent to stabilize the flexible
loop in a favorable conformation. This stabilizing interaction was
not expected to be important in TbcatB; indeed TbcatB was
tolerant of a wide range of substitutions at this position on the
inhibitor scaffold.
An interesting aspect of mammalian cathepsin B-like enzyme
structure is the presence of two salt bridges (His110-Asp22 and
Arg116-Asp224) that stabilize the ‘‘closed’’ conformation of the
loop in the mature form (Figure 6). Mutations that disrupt
either ion pair are correlated with a major increase in
endopeptidase activity [42], presumably due to a correspond-
ing increase in loop flexibility. While the His-Asp pair is
conserved in TbCatB, Arg116 is substituted for Tyr202 and
Asp224 is substituted for Glu307. In TbCatB, the acidic
Figure 3. The substrate binding sites of TbCatB and mammalian CatBs. Surface and ribbon/ball and stick representations comparing the
substrate binding sites of these two cysteine proteases. TbCatB (green), has a deep and spacious S2 pocket, with Gly328 at the bottom. Human CatB,
a representative member of the mammalian homologs (1GMY - CA030 complex, yellow), has the larger Glu245 at this position and the pocket is
shallower. In Human CatBNsmall molecule complexes, the occluding loop points into the substrate binding site. Conversely, the TbCatB occluding
loop is pulled out of the active site. CA074 from the TbCatB crystal structure is shown in grey to orient the reader.
Figure 4. An acidic functionality around the S2 subsite of
TbCatB. Ribbon/ball and stick illustrating an acidic functionality in the
S2 subsite of TbCatB. CA074 is colored in grey and a bound molecule of
glycerol (from the crystal cryosolution) is colored in yellow.
Structural Analysis of TbCatB and Rhodesain 6 June 2010 | Volume 4 | Issue 6 | e701
Page 6
residue does not interact directly with Tyr202, but instead
stabilizes the occluding loop ataninsertion(relativeto
mammalian enzymes) through an interaction with Asn200
(Figure 6). It is tempting to speculate on the role that these
substitutions might play, if any, on altering the characteristic
pH dependance of cathepsin B activity/inhibition. However, at
present, we have no biochemical evidence to support this
assumption and clearly this is a point that requires further
investigation through mutational analysis.
Cysteine proteases are expressed as inactive ‘‘zymogens’’
containing a ‘‘pro’’-domain that aids in the proper folding of the
full-length protein and suppresses the activity of the catalytic
(mature) domain. Autoproteolysis results in cleavage between the
pro and catalytic domains yielding the fully active, mature
enzyme. Comparison of this TbCatB mature domain with crystal
structures of the mature domains of mammalian cathepsin B
enzymes, as well as the mature domains of rhodesain and papain,
shows that the TbCatB structure has an unusually long N-
Figure 5. The S2 subsites of TbCatB and rhodesain. Superimposition of TbCatBNCA074 and rhodesainNK11002 reveals differences in the S2
subsites of the two enzymes. Rhodesain is colored yellow, TbCatB monomer A is blue and TbCatB monomer B (5A only) is pink. K11002 is included in
grey to orient the reader w.r.t the active site. (A) The rhodesain pocket is partially restricted in comparison with TbCatB due to a Asp.Leu
substitution (B) Ala208 at the bottom of the S2 subsite in rhodesain (Gly328 in TbCatB) makes the pocket shallower (C) The S2 subsite in TbCatB is
further opened due to the conformation of the loop between strands b2 and b3. Glycine residues in the loop are colored purple.
Figure 6. Interactions stabilizing the occluding loop in cathepsin B-like enzymes. Ribbon/ball and stick representations illustrating,
important interactions that stabilize the occluding loop (pale cyan) of (A) Human cathepsin B (1GMY) and (B) TbCatB.
Structural Analysis of TbCatB and Rhodesain 7 June 2010 | Volume 4 | Issue 6 | e701
Page 7
terminus. However, further comparison with parasite cysteine
proteases reveal that an elongated N-terminus is shared with the
malarial proteases falcipain-2 (FP-2) and falcipain-3 (FP-3) [43,44]
(Figure S2A). Superimposition with TbCatB reveals the N-
terminal extension of these proteases to be of similar length to
that found in our structure (16 residues in falcipain-2 and 18
residues in falcipain-3). Furthermore, the extension in TbCatB
establishes several polar and hydrophobic interactions with the L
and R domains of the main a/b fold (Figure S2B), as is observed in
structures of FP-2 and FP-3 (although this results in the malarial
extensions adopting more extended secondary structure). While
comparisons can be drawn between TbCatB and the malarial
proteases, the atypical N-terminus of FP-2 and FP-3 was already
identified before the structures were known, including the lack of a
typical papain-family mature cleavage site [43]. Conversely,
TbCatB does contain such a cleavage site and, contrary to our
findings, residues upstream were expected to form part of the pro-
domain. Our Edman sequencing data suggest the possibility of an
even longer end (33 residues N-terminal to the predicted cleavage
site ‘LPSS’). Analysis of the crystal packing in our TbCatB model
suggests these residues may occupy a nearby solvent channel in the
crystal and are therefore disordered. Alternatively, they may be
lost during crystallization. Comparisons with the human and rat
unactivated zymogens (PDB IDs 1MIR and 3PBH) show that, in
the full-length ‘‘pro’’ form, the equivalent residues form a long
loop and short helix that occlude the active site. The possibility of
an additional 33 residues at the N-terminus of the mature TbCatB
therefore remains an intriguing puzzle. While our sequencing data
exclude the possibility of the recombinant enzyme being activated
during yeast cell culture, we cannot exclude cellular activation of
the endogenous enzyme as expressed by the native parasite. The
Western Blot data show the latter to be larger upon activation than
predicted by sequence analyses but slightly smaller than the
recombinant form. We can only speculate that perhaps the native
enzyme undergoes further processing during expression in T.
brucei. Future experiments will be guided towards shedding further
light on the unusual processing of this parasite cysteine protease.
Supporting Information
Figure S1 Western Blot analysis of TbCatB. An immunoblot of
native TbCatB from cultured parasites (Tb lysate, left) and
recombinant, in-vitro activated TbCatB (tbcatB, right). The crude,
unpurified Tb lysate shows two bands representing the zymogen
(upper) and activated, mature (lower) forms. The purified
recombinant protein sample contains only the mature form.
Found at: doi:10.1371/journal.pntd.0000701.s001 (0.22 MB TIF)
Figure S2 Superimposition of TbCatB, falcipain-2 and falci-
pain-3. (A) Comparison of the N-termini of TbCatB (red),
falcipain-2 (light pink) and falcipain-3 (dark pink) in ribbon
representation. The surface and other secondary structure belong
to TbCatB and are colored as Figure 1. (B) Ribbon and ball and
stick representations detailing interactions made between the N-
terminus of TbCatB and the L and R domains of the enzyme.
Colored as (A), with residues belonging to the N-terminus colored
Found at: doi:10.1371/journal.pntd.0000701.s002 (3.56 MB TIF)
Table S1 Superimposition of TbCatBNCA074 with homologous
cathepsin BNsmall molecule complexes.
Found at: doi:10.1371/journal.pntd.0000701.s003 (0.05 MB
Part of this research was performed at the Stanford Synchrotron Radiation
Lightsource (SSRL), a national user facility operated by Stanford
University on behalf of the U.S. Department of Energy, Office of Basic
Energy Sciences. We thank Clyde Smith for beamline support at the SSRL
and Dick Winant at the Protein And Nucleic Acid (PAN) Facility at
Stanford University Medical Center for N-terminal Edman sequencing of
TbCatB. The authors also thank Dr Mohammed Sajid and Dr Thomas
Stout for critical appraisal of the manuscript. All structure figures were
prepared using PyMOL [45].
Author Contributions
Conceived and designed the experiments: PW LSB. Performed the
experiments: IDK PW RMT ZBM LSB. Analyzed the data: IDK.
Contributed reagents/materials/analysis tools: RMT ZBM. Wrote the
paper: IDK. Contributed valuable discussion: ZBM. Principal investigator
on the study: LSB.
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    • "Other more recent reports have also explored sequence diversification among host and pathogen homologous proteins and studied their therapeutic potential (e.g. (Fox et al., 2009; Jansen et al., 2013; Kerr et al., 2010; Urbaniak et al., 2013; Wang et al., 2012)). In this report, we present a systematic approach to identifying novel drug targets that leverages existing sequence information to expand and improve our knowledge of proteins bearing nematode-specific indels. "
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    • "The lyophilized material of the sponge Plakortis halichondroides was sequentially extracted with three different solvents and the crude extracts were tested for protease inhibitory activity against the following proteases: Human cysteine proteases cathepsin B [11] and L [12], the related parasite enzyme rhodesain [13] from Trypanosoma brucei rhodesiense, and the two cysteine proteases expressed by the SARS coronavirus, namely SARS main protease [14] and SARS papain-like protease [15]. The active crude cyclohexane extract (CY) was further fractionated using column chromatography and finally purified with HPLC to yield the active pure metabolite plakortide E (Figure 1). "
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    • "Both LdonCatB and LmajCatB sequences had 52% and 54% identity with that of TbCatB, respectively. The three-dimensional structure of TbCatB has been determined to 1.6 ˚ A (PDB 3hhi [33]) but there is no structural information available for either LdonCatB or LmajCatB. Calculated models for both LdonCatB and Lmaj- CatB were obtained from combining sequence information of the unknown target structures for LdonCatB and LmajCatB with the known model of TbCatB. "
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