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PDBsum entry 1tyz

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1tyz
Jmol
Contents
Protein chains
331 a.a. *
Ligands
SO4 ×4
PLP ×4
Waters ×323
* Residue conservation analysis
PDB id:
1tyz
Name: Hydrolase
Title: Crystal structure of 1-aminocyclopropane-1-carboyxlate deami pseudomonas
Structure: 1-aminocyclopropane-1-carboxylate deaminase. Chain: a, b, c, d. Synonym: acc deaminase. Engineered: yes
Source: Pseudomonas sp.. Organism_taxid: 74568. Strain: acp. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.00Å     R-factor:   0.215     R-free:   0.251
Authors: S.Karthikeyan,Q.Zhou,Z.Zhao,C.L.Kao,Z.Tao,H.Robinson,H.W.Liu
Key ref:
S.Karthikeyan et al. (2004). Structural analysis of Pseudomonas 1-aminocyclopropane-1-carboxylate deaminase complexes: insight into the mechanism of a unique pyridoxal-5'-phosphate dependent cyclopropane ring-opening reaction. Biochemistry, 43, 13328-13339. PubMed id: 15491139 DOI: 10.1021/bi048878g
Date:
08-Jul-04     Release date:   02-Nov-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q00740  (1A1D_PSEUD) -  1-aminocyclopropane-1-carboxylate deaminase
Seq:
Struc:
338 a.a.
331 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.5.99.7  - 1-aminocyclopropane-1-carboxylate deaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 1-aminocyclopropane-1-carboxylate + H2O = 2-oxobutanoate + NH3
1-aminocyclopropane-1-carboxylate
+ H(2)O
= 2-oxobutanoate
+ NH(3)
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.75% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     amine catabolic process   2 terms 
  Biochemical function     hydrolase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi048878g Biochemistry 43:13328-13339 (2004)
PubMed id: 15491139  
 
 
Structural analysis of Pseudomonas 1-aminocyclopropane-1-carboxylate deaminase complexes: insight into the mechanism of a unique pyridoxal-5'-phosphate dependent cyclopropane ring-opening reaction.
S.Karthikeyan, Q.Zhou, Z.Zhao, C.L.Kao, Z.Tao, H.Robinson, H.W.Liu, H.Zhang.
 
  ABSTRACT  
 
1-Aminocyclopropane-1-carboxylate (ACC) deaminase is a pyridoxal 5'-phosphate (PLP) dependent enzyme catalyzing the opening of the cyclopropane ring of ACC to give alpha-ketobutyric acid and ammonia as the products. This ring cleavage reaction is unusual because the substrate, ACC, contains no abstractable alpha-proton and the carboxyl group is retained in the product. How the reaction is initiated to generate an alpha-carbanionic intermediate, which is the common entry for most PLP-dependent reactions, is not obvious. To gain insight into this unusual ring-opening reaction, we have solved the crystal structures of ACC deaminase from Pseudomonas sp. ACP in complex with substrate ACC, an inhibitor, 1-aminocyclopropane-1-phosphonate (ACP), the product alpha-ketobutyrate, and two d-amino acids. Several notable observations of these structural studies include the following: (1) a typically elusive gem-diamine intermediate is trapped in the enzyme complex with ACC or ACP; (2) Tyr294 is in close proximity (3.0 A) to the pro-S methylene carbon of ACC in the gem-diamine complexes, implicating a direct role of this residue in the ring-opening reaction; (3) Tyr294 may also be responsible for the abstraction of the alpha-proton from d-amino acids, a prelude to the subsequent deamination reaction; (4) the steric hindrance precludes accessibility of active site functional groups to the l-amino acid substrates and may account for the stereospecificity of this enzyme toward d-amino acids. These structural data provide evidence favoring a mechanism in which the ring cleavage is induced by a nucleophilic attack at the pro-S beta-methylene carbon of ACC, with Tyr294 as the nucleophile. However, these observations are also consistent with an alternative mechanistic possibility in which the ring opening is acid-catalyzed and may be facilitated by charge relay through PLP, where Tyr294 functions as a general acid. The results of mutagenesis studies corroborated the assigned critical role for Tyr294 in the catalysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18825405 B.Todorovic, and B.R.Glick (2008).
The interconversion of ACC deaminase and D: -cysteine desulfhydrase by directed mutagenesis.
  Planta, 229, 193-205.  
17573137 M.Arshad, M.Saleem, and S.Hussain (2007).
Perspectives of bacterial ACC deaminase in phytoremediation.
  Trends Biotechnol, 25, 356-362.  
17665234 M.Saleem, M.Arshad, S.Hussain, and A.S.Bhatti (2007).
Perspective of plant growth promoting rhizobacteria (PGPR) containing ACC deaminase in stress agriculture.
  J Ind Microbiol Biotechnol, 34, 635-648.  
16269802 N.Hontzeas, A.O.Richardson, A.Belimov, V.Safronova, M.M.Abu-Omar, and B.R.Glick (2005).
Evidence for horizontal transfer of 1-aminocyclopropane-1-carboxylate deaminase genes.
  Appl Environ Microbiol, 71, 7556-7558.  
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.