PDBsum entry 1o59

Go to PDB code: 
protein links
Hydrolase PDB id
Protein chain
318 a.a. *
Waters ×218
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of allantoicase (yir029w) from saccharomyc cerevisiae at 2.40 a resolution
Structure: Allantoicase. Chain: a. Synonym: allantoate amidinohydrolase. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: yir029w. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
2.40Å     R-factor:   0.178     R-free:   0.222
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
Q.Xu et al. (2004). Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 A resolution. Proteins, 56, 619-624. PubMed id: 15229895 DOI: 10.1002/prot.20164
22-Aug-03     Release date:   02-Sep-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P25335  (ALLC_YEAST) -  Allantoicase
343 a.a.
318 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

AMP Catabolism
      Reaction: Allantoate + H2O = (S)-ureidoglycolate + urea
+ H(2)O
= (S)-ureidoglycolate
+ urea
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     allantoin catabolic process   2 terms 
  Biochemical function     hydrolase activity     2 terms  


DOI no: 10.1002/prot.20164 Proteins 56:619-624 (2004)
PubMed id: 15229895  
Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 A resolution.
Q.Xu, R.Schwarzenbacher, R.Page, E.Sims, P.Abdubek, E.Ambing, T.Biorac, L.S.Brinen, J.Cambell, J.M.Canaves, H.J.Chiu, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, R.Floyd, A.Godzik, C.Grittini, S.K.Grzechnik, E.Hampton, L.Jaroszewski, C.Karlak, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, S.A.Lesley, I.Levin, D.McMullan, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, J.Ouyang, K.Quijano, R.Reyes, F.Rezezadeh, A.Robb, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, F.von Delft, X.Wang, B.West, G.Wolf, K.O.Hodgson, J.Wooley, I.A.Wilson.
No abstract given.

  Selected figure(s)  
Figure 1.
Figure 1. Crystal structure of YIR029W. A: Stereo ribbon diagram of Saccharomyces cerevisiae YIR029W color coded from N-terminus (blue) to C-terminus (red) showing the domain organization. Helices H1-H7, and -strands ( 1- 24) in -sheets A-F are indicated. Residue numbers at the beginning and end of missing loops are indicated. B: Diagram showing the secondary structure elements in YIR029W superimposed on its primary sequence. The disordered regions are depicted by a dashed line with the corresponding sequence in brackets. The -sheet designation of the individual -strands are indicated by a red A-F and -hairpins are depicted as red loops.
Figure 2.
Figure 2. A: The YIR029W hexamer in surface representation, shown normal and parallel to the three-fold. Upper and lower trimers are colored grey and green, respectively. One subunit of the gray trimers is shown in blue and the clusters of conserved residues are highlighted in yellow. B: Ribbon diagram of a superposition of YIR029W AR1 (residues 1-187) in yellow and AR2 (residues 193-343) in blue. The cluster of conserved residues in AR1 and AR2 (labels shown in brackets) is shown in ball and stick. C: Ribbon diagram of a superposition of YIR029W AR2 (residues 193-343) in blue and the galactose-binding domain (PDB:1euu) in white with bound substrate (D-galactose) The cluster of conserved residues in AR2 (blue) and the D-galactose (white) are shown in ball and stick.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 56, 619-624) copyright 2004.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16114032 S.Raymond, A.Tocilj, E.Ajamian, Y.Li, M.N.Hung, A.Matte, and M.Cygler (2005).
Crystal structure of ureidoglycolate hydrolase (AllA) from Escherichia coli O157:H7.
  Proteins, 61, 454-459.
PDB code: 1yqc
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.