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PDBsum entry 2o0t

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protein ligands Protein-protein interface(s) links
Lyase PDB id
2o0t
Jmol
Contents
Protein chains
446 a.a. *
Ligands
SO4 ×2
Waters ×393
* Residue conservation analysis
PDB id:
2o0t
Name: Lyase
Title: The three dimensional structure of diaminopimelate decarboxy mycobacterium tuberculosis reveals a tetrameric enzyme orga
Structure: Diaminopimelate decarboxylase. Chain: a, b, c, d. Synonym: dap decarboxylase. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv. Gene: lysa. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.33Å     R-factor:   0.192     R-free:   0.241
Authors: S.Weyand,G.Kefala,M.S.Weiss,Tb Structural Genomics Consortiu
Key ref: S.Weyand et al. (2009). The three-dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation. J Struct Funct Genomics, 10, 209-217. PubMed id: 19543810
Date:
28-Nov-06     Release date:   13-Feb-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam  
P9WIU7  (DCDA_MYCTU) -  Diaminopimelate decarboxylase
Seq:
Struc:
447 a.a.
446 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.4.1.1.20  - Diaminopimelate decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Lysine biosynthesis (later stages)
      Reaction: Meso-2,6-diaminoheptanedioate = L-lysine + CO2
Meso-2,6-diaminoheptanedioate
= L-lysine
+ CO(2)
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cell wall   1 term 
  Biological process     growth   4 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
J Struct Funct Genomics 10:209-217 (2009)
PubMed id: 19543810  
 
 
The three-dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation.
S.Weyand, G.Kefala, D.I.Svergun, M.S.Weiss.
 
  ABSTRACT  
 
The three-dimensional structure of the enzyme diaminopimelate decarboxylase from Mycobacterium tuberculosis has been determined in a new crystal form and refined to a resolution of 2.33 A. The monoclinic crystals contain one tetramer exhibiting D(2)-symmetry in the asymmetric unit. The tetramer exhibits a donut-like structure with a hollow interior. All four active sites are accessible only from the interior of the tetrameric assembly. Small-angle X-ray scattering indicates that in solution the predominant oligomeric species of the protein is a dimer, but also that higher oligomers exist at higher protein concentrations. The observed scattering data are best explained by assuming a dimer-tetramer equilibrium with about 7% tetramers present in solution. Consequently, at the elevated protein concentrations in the crowded environment inside the cell the observed tetramer may constitute the biologically relevant functional unit of the enzyme.