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PDBsum entry 2yid

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
2yid
Jmol
Contents
Protein chains
844 a.a.
Ligands
TD7 ×4
Metals
_CA ×4
_MG ×4
Waters ×730
PDB id:
2yid
Name: Lyase
Title: Crystal structure of the suca domain of mycobacterium smegmatis alpha-ketoglutarate decarboxylase in complex with the enamine-thdp intermediate
Structure: 2-oxoglutarate decarboxylase. Chain: a, b, c, d. Fragment: residues 361-1227. Synonym: 2-oxoglutarate carboxy-lyase, alpha-ketoglutarate decarboxylase, kdh. Engineered: yes
Source: Mycobacterium smegmatis. Organism_taxid: 1772. Strain: mc2155. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: plyss.
Resolution:
2.25Å     R-factor:   0.193     R-free:   0.223
Authors: T.Wagner,M.Bellinzoni,A.M.Wehenkel,H.M.O'Hare,P.M.Alzari
Key ref: T.Wagner et al. (2011). Functional plasticity and allosteric regulation of α-ketoglutarate decarboxylase in central mycobacterial metabolism. Chem Biol, 18, 1011-1020. PubMed id: 21867916 DOI: 10.1016/j.chembiol.2011.06.004
Date:
11-May-11     Release date:   15-Jun-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
A0R2B1  (KGD_MYCS2) -  Multifunctional 2-oxoglutarate metabolism enzyme
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1227 a.a.
844 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.1.2.4.2  - Oxoglutarate dehydrogenase (succinyl-transferring).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Oxo-acid dehydrogenase complexes
      Reaction: 2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO2
2-oxoglutarate
+ [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine
= [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine
+ CO(2)
      Cofactor: Thiamine diphosphate
Thiamine diphosphate
Bound ligand (Het Group name = TD7) matches with 78.79% similarity
   Enzyme class 3: E.C.2.2.1.5  - 2-hydroxy-3-oxoadipate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: 2-oxoglutarate + glyoxylate = 2-hydroxy-3-oxoadipate + CO2
2-oxoglutarate
+ glyoxylate
= 2-hydroxy-3-oxoadipate
+ CO(2)
      Cofactor: Thiamine diphosphate
Thiamine diphosphate
   Enzyme class 4: E.C.2.3.1.61  - Dihydrolipoyllysine-residue succinyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: Succinyl-CoA + enzyme N6-(dihydrolipoyl)lysine = CoA + enzyme N6- (S-succinyldihydrolipoyl)lysine
Succinyl-CoA
+ enzyme N(6)-(dihydrolipoyl)lysine
= CoA
+ enzyme N(6)- (S-succinyldihydrolipoyl)lysine
   Enzyme class 5: E.C.4.1.1.71  - 2-oxoglutarate decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-oxoglutarate = succinate semialdehyde + CO2
2-oxoglutarate
= succinate semialdehyde
+ CO(2)
      Cofactor: Thiamine diphosphate
Thiamine diphosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     thiamine pyrophosphate binding     3 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.chembiol.2011.06.004 Chem Biol 18:1011-1020 (2011)
PubMed id: 21867916  
 
 
Functional plasticity and allosteric regulation of α-ketoglutarate decarboxylase in central mycobacterial metabolism.
T.Wagner, M.Bellinzoni, A.Wehenkel, H.M.O'Hare, P.M.Alzari.
 
  ABSTRACT  
 
No abstract given.