2XE4

Structure of Oligopeptidase B from Leishmania major


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

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.Biol.Chem. 285: 39249

  • DOI: 10.1074/jbc.M110.156679

  • 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 a ...

    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. Karen.McLuskey@glasgow.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OLIGOPEPTIDASE B
A
751Leishmania majorMutation(s): 1 
Gene Names: OPB
EC: 3.4.21.83
Find proteins for Q4QHU7 (Leishmania major)
Go to UniProtKB:  Q4QHU7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ANTIPAIN
B
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PGR
Query on PGR

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A
R-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-GSVOUGTGSA-N
 Ligand Interaction
PGO
Query on PGO

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A
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002097
Query on PRD_002097
BAntipainOligopeptide / Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.140 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 95.478α = 90.00
b = 142.776β = 90.00
c = 208.919γ = 90.00
Software Package:
Software NamePurpose
autoSHARPphasing
SHELXCDphasing
d*TREKdata reduction
SHELXDphasing
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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