1QVZ

Crystal structure of the S. cerevisiae YDR533c protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.str.2004.02.030
  • Primary Citation of Related Structures:  

  • 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 belongin ...

    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, B√Ętiment 34, 1 Avenue de la Terrasse, 91198 Gif sur Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YDR533c protein
A, B
237Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 4 
Gene Names: HSP31
EC: 4.2.1.130
Find proteins for Q04432 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04432
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 61.404α = 90.00
b = 165.927β = 90.00
c = 47.807γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-30
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance