2XE4 | pdb_00002xe4

Structure of Oligopeptidase B from Leishmania major

• PDB DOI: https://doi.org/10.2210/pdb2XE4/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Leishmania major, Actinomycetes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-05-11 Released: 2010-10-06 
• Deposition Author(s): McLuskey, K., Paterson, N.G., Bland, N.D., Mottram, J.C., Isaacs, N.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.178 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Literature

Crystal Structure of Leishmania Major Oligopeptidase B Gives Insight Into the Enzymatic Properties of a Trypanosomatid Virulence Factor.

Mcluskey, K., Paterson, N.G., Bland, N.D., Isaacs, N.W., Mottram, J.C.

(2010) J Biological Chem 285: 39249

• PubMed: 20926390 
• DOI: https://doi.org/10.1074/jbc.M110.156679
• Primary Citation Related Structures: 
  2XE4


• PubMed Abstract: 
  

  Oligopeptidase B (OPB) is a serine peptidase with dibasic substrate specificity. It is found in bacteria, plants, and trypanosomatid pathogens, where it has been identified as a virulence factor and potential drug target. In this study we expressed active recombinant Leishmania major OPB and provide the first structure of an oligopeptidase B at high resolution. The crystallographic study reveals that OPB comprises two domains, a catalytic and a propeller domain, linked together by a hinge region. The structure has been determined in complex with the oligopeptide, protease-inhibitor antipain, giving detailed information on the enzyme active site and extended substrate binding pockets. It shows that Glu-621 plays a critical role in the S1 binding pocket and, along with Phe-603, is largely responsible for the enzyme substrate specificity in P1. In the S2 binding pocket, Tyr-499 was shown to be important for substrate stability. The structure also allowed an investigation into the function of residues highlighted in other studies including Glu-623, which was predicted to be involved in the S1 binding pocket but is found forming an inter-domain hydrogen bond. Additional important salt bridges/hydrogen bonds between the two domains were observed, highlighting the significance of the domain interface in OPB. This work provides a foundation for the study of the role of OPBs as virulence factors in trypanosomatids. It could facilitate the development of specific OPB inhibitors with therapeutic potential by exploiting its unique substrate recognition properties as well as providing a model for OPBs in general.

---

Organizational Affiliation: 
• Westchem School of Chemistry, University of Glasgow, Glasgow G12 8TA, Scotland, United Kingdom. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.97 kDa 
• Atom Count: 7,215 
• Modeled Residue Count: 725 
• Deposited Residue Count: 755 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OLIGOPEPTIDASE B	A	751	Leishmania major	Mutation(s): 1  EC: 3.4.21.83 (PDB Primary Data), 3.4.21 (UniProt)
UniProt
Find proteins for Q4QHU7 (Leishmania major) Explore Q4QHU7  Go to UniProtKB:  Q4QHU7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIPAIN	B	4	Actinomycetes	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	JB [auth A], KB [auth A], LB [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
PGR	AA [auth A], AB [auth A], BA [auth A], BB [auth A], CA [auth A], CB [auth A], DA [auth A], DB [auth A], EA [auth A], EB [auth A], FA [auth A], FB [auth A], GA [auth A], GB [auth A], HA [auth A], HB [auth A], IA [auth A], IB [auth A], JA [auth A], KA [auth A], LA [auth A], M [auth A], MA [auth A], NA [auth A], O [auth A], OA [auth A], P [auth A], PA [auth A], Q [auth A], QA [auth A], R [auth A], RA [auth A], S [auth A], SA [auth A], T [auth A], TA [auth A], U [auth A], UA [auth A], V [auth A], VA [auth A], W [auth A], WA [auth A], X [auth A], XA [auth A], Y [auth A], YA [auth A], Z [auth A], ZA [auth A]	R-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-GSVOUGTGSA-N
PGO	N [auth A]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N
CL	MB [auth A], OB [auth A], QB [auth A], RB [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	NB [auth A], PB [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
RGL	B	L-PEPTIDE LINKING	C6 H15 N4 O		ARG

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002097	B	Antipain	Oligopeptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.178 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.478	α = 90
b = 142.776	β = 90
c = 208.919	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
SCALA	data scaling
autoSHARP	phasing
SHELXCD	phasing
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-06 
Deposition Author(s): McLuskey, K., Paterson, N.G., Bland, N.D., Mottram, J.C., Isaacs, N.W.

Revision History  

• Version 1.0: 2010-10-06
  Type: Initial release
  
• Version 1.1: 2011-08-10
  Changes: Database references, Structure summary, Version format compliance
• Version 1.2: 2012-11-30
  Changes: Other
• Version 1.3: 2013-08-07
  Changes: Other
• Version 2.0: 2019-05-15
  Changes: Advisory, Data collection, Derived calculations, Other, Polymer sequence
• Version 2.1: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary