7OB1

OLIGOPEPTIDASE B FROM S. PROTEOMACULANS WITH MODIFIED HINGE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

First Crystal Structure of Bacterial Oligopeptidase B in an Intermediate State: The Roles of the Hinge Region Modification and Spermine.

Petrenko, D.E.Timofeev, V.I.Britikov, V.V.Britikova, E.V.Kleymenov, S.Y.Vlaskina, A.V.Kuranova, I.P.Mikhailova, A.G.Rakitina, T.V.

(2021) Biology (Basel) 10

  • DOI: https://doi.org/10.3390/biology10101021
  • Primary Citation of Related Structures:  
    7NE4, 7NE5, 7OB1

  • PubMed Abstract: 

    Oligopeptidase B (OpB) is a two-domain, trypsin-like serine peptidase belonging to the S9 prolyloligopeptidase (POP) family. Two domains are linked by a hinge region that participates in the transition of the enzyme between two major states-closed and open-in which domains and residues of the catalytic triad are located close to each other and separated, respectively. In this study, we described, for the first time, a structure of OpB from bacteria obtained for an enzyme from Serratia proteomaculans with a modified hinge region (PSPmod). PSPmod was crystallized in a conformation characterized by a disruption of the catalytic triad together with a domain arrangement intermediate between open and closed states found in crystals of ligand-free and inhibitor-bound POP, respectively. Two additional derivatives of PSPmod were crystallized in the same conformation. Neither wild-type PSP nor its corresponding mutated variants were susceptible to crystallization, indicating that the hinge region modification was key in the crystallization process. The second key factor was suggested to be polyamine spermine since all crystals were grown in its presence. The influences of the hinge region modification and spermine on the conformational state of PSP in solution were evaluated by small-angle X-ray scattering. SAXS showed that, in solution, wild-type PSP adopted the open state, spermine caused the conformational transition to the intermediate state, and spermine-free PSPmod contained molecules in the open and intermediate conformations in dynamic equilibrium.


  • Organizational Affiliation

    National Research Center "Kurchatov Institute", 123182 Moscow, Russia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oligopeptidase B677Serratia proteamaculansMutation(s): 0 
Gene Names: opdB
UniProt
Find proteins for B3VI58 (Serratia proteamaculans)
Explore B3VI58 
Go to UniProtKB:  B3VI58
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3VI58
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.21α = 90
b = 101.02β = 90
c = 108.89γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
BALBESphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2022-11-02
    Changes: Advisory, Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description