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PDBsum entry 1sg3

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protein Protein-protein interface(s) links
Hydrolase PDB id
1sg3
Jmol
Contents
Protein chains
317 a.a. *
Waters ×124
* Residue conservation analysis
PDB id:
1sg3
Name: Hydrolase
Title: Structure of allantoicase
Structure: Allantoicase. Chain: a, b. Synonym: allantoate amidinohydrolase. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: dal2, alc1, yir029w. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Hexamer (from PDB file)
Resolution:
2.60Å     R-factor:   0.200     R-free:   0.271
Authors: N.Leulliot,S.Quevillon-Cheruel,I.Sorel,M.Graille,P.Meyer, D.Liger,K.Blondeau,J.Janin,H.Van Tilbeurgh
Key ref:
N.Leulliot et al. (2004). Crystal structure of yeast allantoicase reveals a repeated jelly roll motif. J Biol Chem, 279, 23447-23452. PubMed id: 15020593 DOI: 10.1074/jbc.M401336200
Date:
23-Feb-04     Release date:   02-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P25335  (ALLC_YEAST) -  Allantoicase
Seq:
Struc:
343 a.a.
317 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.5.3.4  - Allantoicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
AMP Catabolism
      Reaction: Allantoate + H2O = (S)-ureidoglycolate + urea
Allantoate
+ 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  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M401336200 J Biol Chem 279:23447-23452 (2004)
PubMed id: 15020593  
 
 
Crystal structure of yeast allantoicase reveals a repeated jelly roll motif.
N.Leulliot, S.Quevillon-Cheruel, I.Sorel, M.Graille, P.Meyer, D.Liger, K.Blondeau, J.Janin, H.van Tilbeurgh.
 
  ABSTRACT  
 
Allantoicase (EC 3.5.3.4) catalyzes the conversion of allantoate into ureidoglycolate and urea, one of the final steps in the degradation of purines to urea. The mechanism of most enzymes involved in this pathway, which has been known for a long time, is unknown. In this paper we describe the three-dimensional crystal structure of the yeast allantoicase determined at a resolution of 2.6 A by single anomalous diffraction. This constitutes the first structure for an enzyme of this pathway. The structure reveals a repeated jelly roll beta-sheet motif, also present in proteins of unrelated biochemical function. Allantoicase has a hexameric arrangement in the crystal (dimer of trimers). Analysis of the protein sequence against the structural data reveals the presence of two totally conserved surface patches, one on each jelly roll motif. The hexameric packing concentrates these patches into conserved pockets that probably constitute the active site.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Reaction scheme of the two reactions that are catalyzed by allantoicase.
Figure 3.
FIG. 3. A, representation of the allantoicase dimer in the asymmetric unit. The two subunits are related by a 2-fold axis. The labels of the second subunit are primed. B, ribbon representation of the hexamer generated by P6[3] crystal symmetry. The two subunits of the non-crystallographic dimer are colored in blue and green. The loops containing the regions Ia, IIa, IIIa, and IVa and the regions Ib, IIb, IIIb, and IVb are colored in red and in orange, respectively (same color code as Fig. 2B). The boxed region at the interface is represented in more detail in C. C, detailed representation of the interface between two molecules of the hexamer (B). The interface involves residues from conserved regions I-IV, colored red and orange in modules A and B, respectively (same color code as the other figures). The interface creates a narrow groove lined with conserved residues representing the putative catalytic site.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 23447-23452) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19901092 F.Robin, N.Aggoune-Khinache, J.Delmas, M.Naim, and R.Bonnet (2010).
Novel VIM metallo-beta-lactamase variant from clinical isolates of Enterobacteriaceae from Algeria.
  Antimicrob Agents Chemother, 54, 466-470.  
17220412 F.Robin, J.Delmas, C.Schweitzer, O.Tournilhac, O.Lesens, C.Chanal, and R.Bonnet (2007).
Evolution of TEM-type enzymes: biochemical and genetic characterization of two new complex mutant TEM enzymes, TEM-151 and TEM-152, from a single patient.
  Antimicrob Agents Chemother, 51, 1304-1309.  
16333637 A.Muñoz, M.J.Raso, M.Pineda, and P.Piedras (2006).
Degradation of ureidoglycolate in French bean (Phaseolus vulgaris) is catalysed by a ubiquitous ureidoglycolate urea-lyase.
  Planta, 224, 175-184.  
16801418 F.Robin, J.Delmas, M.Archambaud, C.Schweitzer, C.Chanal, and R.Bonnet (2006).
CMT-type beta-lactamase TEM-125, an emerging problem for extended-spectrum beta-lactamase detection.
  Antimicrob Agents Chemother, 50, 2403-2408.  
16436733 J.Delmas, F.Robin, F.Carvalho, C.Mongaret, and R.Bonnet (2006).
Prediction of the evolution of ceftazidime resistance in extended-spectrum beta-lactamase CTX-M-9.
  Antimicrob Agents Chemother, 50, 731-738.  
16251281 F.Robin, J.Delmas, C.Chanal, D.Sirot, J.Sirot, and R.Bonnet (2005).
TEM-109 (CMT-5), a natural complex mutant of TEM-1 beta-lactamase combining the amino acid substitutions of TEM-6 and TEM-33 (IRT-5).
  Antimicrob Agents Chemother, 49, 4443-4447.  
16189109 J.Delmas, F.Robin, F.Bittar, C.Chanal, and R.Bonnet (2005).
Unexpected enzyme TEM-126: role of mutation Asp179Glu.
  Antimicrob Agents Chemother, 49, 4280-4287.  
15930617 N.Leulliot, L.Trésaugues, M.Bremang, I.Sorel, N.Ulryck, M.Graille, I.Aboulfath, A.Poupon, D.Liger, S.Quevillon-Cheruel, J.Janin, and H.van Tilbeurgh (2005).
High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all?
  Acta Crystallogr D Biol Crystallogr, 61, 664-670.  
16195557 N.Leulliot, S.Quevillon-Cheruel, M.Graille, M.Schiltz, K.Blondeau, J.Janin, and H.Van Tilbeurgh (2005).
Crystal structure of yeast YER010Cp, a knotable member of the RraA protein family.
  Protein Sci, 14, 2751-2758.
PDB code: 2c5q
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
15465324 G.R.Vasta, H.Ahmed, and E.W.Odom (2004).
Structural and functional diversity of lectin repertoires in invertebrates, protochordates and ectothermic vertebrates.
  Curr Opin Struct Biol, 14, 617-630.  
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.