PDBsum entry 1vkh

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Hydrolase PDB id
Protein chains
261 a.a. *
GOL ×2
Waters ×458
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of a putative serine hydrolase (ydr428c) f saccharomyces cerevisiae at 1.85 a resolution
Structure: Putative serine hydrolase. Chain: a, b. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ydr428c. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.85Å     R-factor:   0.145     R-free:   0.189
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
J.W.Arndt et al. (2005). Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution. Proteins, 58, 755-758. PubMed id: 15624212 DOI: 10.1002/prot.20336
20-May-04     Release date:   08-Jun-04    
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Protein chains
Pfam   ArchSchema ?
Q04066  (BNA7_YEAST) -  Kynurenine formamidase
261 a.a.
261 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Arylformamidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Tryptophan Catabolism
      Reaction: N-formyl-L-kynurenine + H2O = formate + L-kynurenine
+ H(2)O
= formate
+ L-kynurenine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cellular_component   1 term 
  Biological process     metabolic process   5 terms 
  Biochemical function     hydrolase activity     2 terms  


DOI no: 10.1002/prot.20336 Proteins 58:755-758 (2005)
PubMed id: 15624212  
Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution.
J.W.Arndt, R.Schwarzenbacher, R.Page, P.Abdubek, E.Ambing, T.Biorac, J.M.Canaves, H.J.Chiu, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, A.Godzik, C.Grittini, S.K.Grzechnik, J.Hale, E.Hampton, G.W.Han, J.Haugen, M.Hornsby, H.E.Klock, E.Koesema, A.Kreusch, P.Kuhn, L.Jaroszewski, S.A.Lesley, I.Levin, D.McMullan, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, E.Nigoghossian, J.Ouyang, W.S.Peti, K.Quijano, R.Reyes, E.Sims, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, F.von Delft, X.Wang, B.West, A.White, G.Wolf, Q.Xu, O.Zagnitko, K.O.Hodgson, J.Wooley, I.A.Wilson.
No abstract given.

  Selected figure(s)  
Figure 1.
Figure 1. Crystal structure of YDR428C. A: Stereoview of ribbon diagram of Saccharomyces cerevisiae YDR428C color coded from N-terminus (blue) to C-terminus (red) showing the domain organization. -Helices H1-H12, and -strands ( 1- 7) are indicated. B: Diagram showing the secondary structure elements in YDR428C superimposed on its primary sequence. The -helices, 3[10]-helices, -sheet strands (red A), -bulges, and -turns are indicated. The disordered regions are depicted by a dashed line with the corresponding sequence in brackets.
Figure 2.
Figure 2. A: Ribbon diagram of a superposition of YDR428C (blue) and P. fluorescens carboxylesterase (grey). Residues of the catalytic triad, shown in ball and stick, indicate the active site location. B: Same as A, but a close up view of the catalytic triad. Active site residues as observed in P. fluorescens carboxylesterase (PDB 1auo; grey; P. fluorescens residues shown in parenthesis) and their counterparts in YDR428C (blue) are shown in ball and stick. Hydrogen bond interactions and distances are indicated. C: Ribbon diagram of the YDR428C dimer. 7 strands and helices H10 and H12 forming part of the dimer interface and locations of active sites (arrow) are indicated.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 58, 755-758) copyright 2005.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  16754966 C.Y.Yang, K.H.Chin, C.C.Chou, A.H.Wang, and S.H.Chou (2006).
Structure of XC6422 from Xanthomonas campestris at 1.6 A resolution: a small serine alpha/beta-hydrolase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 498-503.
PDB code: 2fuk
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