PDBsum entry 1qvz

Go to PDB code: 
protein Protein-protein interface(s) links
Structural genomics, unknown function PDB id
Protein chains
236 a.a. *
Waters ×422
* Residue conservation analysis
PDB id:
Name: Structural genomics, unknown function
Title: Crystal structure of the s. Cerevisiae ydr533c protein
Structure: Ydr533c protein. Chain: a, b. Engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ydr533c. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
1.85Å     R-factor:   0.191     R-free:   0.215
Authors: M.Graille,N.Leulliot,S.Quevillon-Cheruel,H.Van Tilbeurgh
Key ref:
M.Graille et al. (2004). Crystal structure of the YDR533c S. cerevisiae protein, a class II member of the Hsp31 family. Structure, 12, 839-847. PubMed id: 15130476 DOI: 10.1016/j.str.2004.02.030
29-Aug-03     Release date:   30-Mar-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q04432  (HSP31_YEAST) -  Glutathione-independent glyoxalase HSP31
237 a.a.
236 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - D-lactate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (R)-lactate = methylglyoxal + H2O
= methylglyoxal
+ H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   3 terms 
  Biological process     cellular response to oxidative stress   4 terms 
  Biochemical function     lyase activity     2 terms  


    Added reference    
DOI no: 10.1016/j.str.2004.02.030 Structure 12:839-847 (2004)
PubMed id: 15130476  
Crystal structure of the YDR533c S. cerevisiae protein, a class II member of the Hsp31 family.
M.Graille, S.Quevillon-Cheruel, N.Leulliot, C.Z.Zhou, la Sierra Gallay, L.Jacquamet, J.L.Ferrer, D.Liger, A.Poupon, J.Janin, H.van Tilbeurgh.
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.
  Selected figure(s)  
Figure 3.
Figure 3. The Putative Catalytic Triad(A) Hydrophobic surface representation of the YDR533c dimer. Polar and hydrophobic residues are colored in white and red, respectively. The cysteine 138 side chain is shown as sticks. The putative active site pocket from one monomer is highlighted by dotted lines.(B) Superimposition of the YDR533c (green), E. coli Hsp31 (yellow), and PhPI (blue) catalytic triads (the proper triad acidic residue corresponds to Glu170). The DJ-1 putative catalytic dyad is show in pink. Only the YD533c numbering is indicated.
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 839-847) copyright 2004.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19416074 T.C.Terwilliger, D.Stuart, and S.Yokoyama (2009).
Lessons from structural genomics.
  Annu Rev Biophys, 38, 371-383.  
18227433 F.R.Salsbury, S.T.Knutson, L.B.Poole, and J.S.Fetrow (2008).
Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid.
  Protein Sci, 17, 299-312.  
17847089 K.Goyal, and S.C.Mande (2008).
Exploiting 3D structural templates for detection of metal-binding sites in protein structures.
  Proteins, 70, 1206-1218.  
  17277453 W.Liu, Y.Y.Zhou, M.K.Teng, and C.Z.Zhou (2007).
Purification, crystallization and preliminary X-ray analysis of Hsp33 from Saccharomyces cerevisiae.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 114-116.  
16731983 S.Quevillon-Cheruel, N.Leulliot, M.Graille, K.Blondeau, J.Janin, and H.van Tilbeurgh (2006).
Crystal structure of the yeast His6 enzyme suggests a reaction mechanism.
  Protein Sci, 15, 1516-1521.
PDB code: 2agk
16489413 T.Miura, H.Minegishi, R.Usami, and F.Abe (2006).
Systematic analysis of HSP gene expression and effects on cell growth and survival at high hydrostatic pressure in Saccharomyces cerevisiae.
  Extremophiles, 10, 279-284.  
15608122 C.Z.Zhou, P.Meyer, S.Quevillon-Cheruel, I.L.De La Sierra-Gallay, B.Collinet, M.Graille, K.Blondeau, J.M.François, N.Leulliot, I.Sorel, A.Poupon, J.Janin, and H.Van Tilbeurgh (2005).
Crystal structure of the YML079w protein from Saccharomyces cerevisiae reveals a new sequence family of the jelly-roll fold.
  Protein Sci, 14, 209-215.
PDB codes: 1xe7 1xe8
15802654 S.Quevillon-Cheruel, N.Leulliot, M.Graille, N.Hervouet, F.Coste, H.Bénédetti, C.Zelwer, J.Janin, and H.Van Tilbeurgh (2005).
Crystal structure of yeast YHR049W/FSH1, a member of the serine hydrolase family.
  Protein Sci, 14, 1350-1356.
PDB code: 1ycd
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.