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PDBsum entry 3b8i

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
3b8i
Jmol
Contents
Protein chains
(+ 0 more) 284 a.a. *
Ligands
OXL ×6
GOL ×8
Metals
_MG ×6
Waters ×1859
* Residue conservation analysis
PDB id:
3b8i
Name: Lyase
Title: Crystal structure of oxaloacetate decarboxylase from pseudom aeruginosa (pa4872) in complex with oxalate and mg2+.
Structure: Pa4872 oxaloacetate decarboxylase. Chain: a, b, c, d, e, f. Engineered: yes
Source: Pseudomonas aeruginosa. Organism_taxid: 208964. Strain: pao1. Gene: dnase1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.90Å     R-factor:   0.197     R-free:   0.249
Authors: B.C.Narayanan,O Herzberg
Key ref: B.C.Narayanan et al. (2008). Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily. Biochemistry, 47, 167-182. PubMed id: 18081320
Date:
01-Nov-07     Release date:   01-Jan-08    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9HUU1  (OADC_PSEAE) -  Oxaloacetate decarboxylase
Seq:
Struc:
287 a.a.
284 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.1.1.3  - Oxaloacetate decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Oxaloacetate = pyruvate + CO2
Oxaloacetate
=
pyruvate
Bound ligand (Het Group name = OXL)
matches with 71.43% similarity
+ CO(2)
      Cofactor: Biotin; Mn(2+) or Na(+)
Biotin
Mn(2+)
or Na(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carboxylic acid metabolic process   3 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
Biochemistry 47:167-182 (2008)
PubMed id: 18081320  
 
 
Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily.
B.C.Narayanan, W.Niu, Y.Han, J.Zou, P.S.Mariano, D.Dunaway-Mariano, O.Herzberg.
 
  ABSTRACT  
 
Pseudomonas aeruginosa PA4872 was identified by sequence analysis as a structurally and functionally novel member of the PEP mutase/isocitrate lyase superfamily and therefore targeted for investigation. Substrate screens ruled out overlap with known catalytic functions of superfamily members. The crystal structure of PA4872 in complex with oxalate (a stable analogue of the shared family alpha-oxyanion carboxylate intermediate/transition state) and Mg2+ was determined at 1.9 A resolution. As with other PEP mutase/isocitrate lyase superfamily members, the protein assembles into a dimer of dimers with each subunit adopting an alpha/beta barrel fold and two subunits swapping their barrel's C-terminal alpha-helices. Mg2+ and oxalate bind in the same manner as observed with other superfamily members. The active site gating loop, known to play a catalytic role in the PEP mutase and lyase branches of the superfamily, adopts an open conformation. The Nepsilon of His235, an invariant residue in the PA4872 sequence family, is oriented toward a C(2) oxygen of oxalate analogous to the C(3) of a pyruvyl moiety. Deuterium exchange into alpha-oxocarboxylate-containing compounds was confirmed by 1H NMR spectroscopy. Having ruled out known activities, the involvement of a pyruvate enolate intermediate suggested a decarboxylase activity of an alpha-oxocarboxylate substrate. Enzymatic assays led to the discovery that PA4872 decarboxylates oxaloacetate (kcat = 7500 s(-1) and Km = 2.2 mM) and 3-methyloxaloacetate (kcat = 250 s(-1) and Km = 0.63 mM). Genome context of the fourteen sequence family members indicates that the enzyme is used by select group of Gram-negative bacteria to maintain cellular concentrations of bicarbonate and pyruvate; however the decarboxylation activity cannot be attributed to a pathway common to the various bacterial species.