1QVW

Crystal structure of the S. cerevisiae YDR533c protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Crystal structure of the YDR533c S. cerevisiae protein, a class II member of the Hsp31 family

Graille, M.Quevillon-Cheruel, S.Leulliot, N.Zhou, C.Z.de la Sierra Gallay, I.L.Jacquamet, L.Ferrer, J.L.Liger, D.Poupon, A.Janin, J.van Tilbeurgh, H.

(2004) Structure 12: 839-847

  • DOI: https://doi.org/10.1016/j.str.2004.02.030
  • Primary Citation of Related Structures:  
    1QVV, 1QVW, 1QVZ

  • PubMed Abstract: 

    The ORF YDR533c from Saccharomyces cerevisiae codes for a 25.5 kDa protein of unknown biochemical function. Transcriptome analysis of yeast has shown that this gene is activated in response to various stress conditions together with proteins belonging to the heat shock family. In order to clarify its biochemical function, we determined the crystal structure of YDR533c to 1.85 A resolution by the single anomalous diffraction method. The protein possesses an alpha/beta hydrolase fold and a putative Cys-His-Glu catalytic triad common to a large enzyme family containing proteases, amidotransferases, lipases, and esterases. The protein has strong structural resemblance with the E. coli Hsp31 protein and the intracellular protease I from Pyrococcus horikoshii, which are considered class I and class III members of the Hsp31 family, respectively. Detailed structural analysis strongly suggests that the YDR533c protein crystal structure is the first one of a class II member of the Hsp31 family.


  • Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, CNRS-UPR 9063, Bâtiment 34, 1 Avenue de la Terrasse, 91198 Gif sur Yvette, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YDR533c protein
A, B
237Saccharomyces cerevisiaeMutation(s): 5 
Gene Names: YDR533c
EC: 4.2.1.130
UniProt
Find proteins for Q04432 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04432 
Go to UniProtKB:  Q04432
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04432
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
A, B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.531α = 90
b = 166.196β = 90
c = 48.295γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-30
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-10-23
    Changes: Structure summary