1IU8 | pdb_00001iu8

The X-ray Crystal Structure of Pyrrolidone-Carboxylate Peptidase from Hyperthermophilic Archaeon Pyrococcus horikoshii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.214 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.187 (DCC) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

The X-ray crystal structure of pyrrolidone-carboxylate peptidase from hyperthermophilic archaea Pyrococcus horikoshii

Sokabe, M.Kawamura, T.Sakai, N.Yao, M.Watanabe, N.Tanaka, I.

(2002) J Struct Funct Genomics 2: 145-154

  • DOI: https://doi.org/10.1023/a:1021257701676
  • Primary Citation Related Structures: 
    1IU8

  • PubMed Abstract: 

    The crystal structure of pyrrolidone-carboxylate peptidase (PCP) from hyperthermophilic archaea Pyrococcus horikoshii (PhoPCP) has been determined at 1.6-A resolution by X-ray crystallography. PCP belongs to the C15 family of cysteine protease, and specifically removes the amino terminal pyroglutamate residue from a wide range of N-terminal-blocking peptides. The crystal structure is very similar to that of other hyperthermophiles, Pyrococcus furiosus and Thermococcus litoralis, and even that from the mesophile, Bacillus amyloliquefaciens. The inter-subunit disulfide bonds, which have been proposed as one of the thermostabilizing factors of the PCP from such hyperthermophiles, was not present in PhoPCP. The result suggests that the thermostability of PhoPCP may be obtained by the accumulation of many weak factors.


  • Organizational Affiliation
    • Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan.

Macromolecule Content 

  • Total Structure Weight: 45.33 kDa 
  • Atom Count: 3,683 
  • Modeled Residue Count: 412 
  • Deposited Residue Count: 412 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pyrrolidone-carboxylate peptidase
A, B
206Pyrococcus horikoshiiMutation(s): 0 
Gene Names: PH0596
EC: 3.4.19.3
UniProt
Find proteins for O58321 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58321 
Go to UniProtKB:  O58321
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO58321
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.214 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.187 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.899α = 90
b = 66.479β = 128.68
c = 76.396γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Refinement description