Prolyl oligopeptidase from Pyrococcus furiosus

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase.

Ellis-Guardiola, K.Rui, H.Beckner, R.L.Srivastava, P.Sukumar, N.Roux, B.Lewis, J.C.

(2019) Biochemistry 58: 1616-1626

  • DOI: https://doi.org/10.1021/acs.biochem.9b00031
  • Primary Citation of Related Structures:  
    5T88, 6CAN

  • PubMed Abstract: 

    Enzymes in the prolyl oligopeptidase family possess unique structures and substrate specificities that are important for their biological activity and for potential biocatalytic applications. The crystal structures of Pyrococcus furiosus ( Pfu) prolyl oligopeptidase (POP) and the corresponding S477C mutant were determined to 1.9 and 2.2 Å resolution, respectively. The wild type enzyme crystallized in an open conformation, indicating that this state is readily accessible, and it contained bound chloride ions and a prolylproline ligand. These structures were used as starting points for molecular dynamics simulations of Pfu POP conformational dynamics. The simulations showed that large-scale domain opening and closing occurred spontaneously, providing facile substrate access to the active site. Movement of the loop containing the catalytically essential histidine into a conformation similar to those found in structures with fully formed catalytic triads also occurred. This movement was modulated by chloride binding, providing a rationale for experimentally observed activation of POP peptidase catalysis by chloride. Thus, the structures and simulations reported in this study, combined with existing biochemical data, provide a number of insights into POP catalysis.

  • Organizational Affiliation

    Department of Chemistry , University of Chicago , Chicago , Illinois 60637 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prolyl endopeptidase
A, B
616Pyrococcus furiosusMutation(s): 1 
Find proteins for Q51714 (Pyrococcus furiosus)
Explore Q51714 
Go to UniProtKB:  Q51714
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ51714
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TRS

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
C4 H12 N O3
Query on PRO

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
T [auth B],
U [auth B]
C5 H9 N O2
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
L [auth B],
M [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.535α = 90
b = 176.757β = 106.03
c = 57.901γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE 1351991
Army Research OfficeUnited States62247-LS
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM008720
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM103403

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.2: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2023-10-04
    Changes: Advisory, Data collection, Database references, Refinement description