5T88

Prolyl oligopeptidase from Pyrococcus furiosus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.902 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1021/acs.biochem.9b00031

  • 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) proly ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prolyl endopeptidase
A, B
616Pyrococcus furiosusMutation(s): 0 
Find proteins for Q51714 (Pyrococcus furiosus)
Go to UniProtKB:  Q51714
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PRO
Query on PRO

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Download CCD File 
A, B
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.902 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.535α = 90.00
b = 176.757β = 106.03
c = 57.901γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesCHE 1351991
USAROUnited States62247-LS
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32 GM008720
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41 GM103403

Revision History 

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence
  • Version 1.2: 2019-04-17
    Type: Data collection, Database references