PDBsum entry 2ozl

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
Protein chains
362 a.a. *
330 a.a. *
TPP ×2
__K ×2
_MG ×2
Waters ×757
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Human pyruvate dehydrogenase s264e variant
Structure: Pyruvate dehydrogenase e1 component alpha subunit, somatic form. Chain: a, c. Fragment: alpha subunit. Synonym: pdhe1-a type i. Engineered: yes. Mutation: yes. Pyruvate dehydrogenase e1 component subunit beta. Chain: b, d.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: pdha1, phe1a. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: pdhb, phe1b.
1.90Å     R-factor:   0.186     R-free:   0.221
Authors: E.M.Ciszak,P.M.Dominiak,M.S.Patel,L.G.Korotchkina
Key ref:
F.Seifert et al. (2007). Phosphorylation of serine 264 impedes active site accessibility in the E1 component of the human pyruvate dehydrogenase multienzyme complex. Biochemistry, 46, 6277-6287. PubMed id: 17474719 DOI: 10.1021/bi700083z
26-Feb-07     Release date:   22-May-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P08559  (ODPA_HUMAN) -  Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial
390 a.a.
362 a.a.*
Protein chains
Pfam   ArchSchema ?
P11177  (ODPB_HUMAN) -  Pyruvate dehydrogenase E1 component subunit beta, mitochondrial
359 a.a.
330 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.  - Pyruvate dehydrogenase (acetyl-transferring).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Oxo-acid dehydrogenase complexes
      Reaction: Pyruvate + [dihydrolipoyllysine-residue acetyltransferase] lipoyllysine = [dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine + CO2
+ [dihydrolipoyllysine-residue acetyltransferase] lipoyllysine
= [dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine
+ CO(2)
      Cofactor: Thiamine diphosphate
Thiamine diphosphate
Bound ligand (Het Group name = TPP) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular vesicular exosome   6 terms 
  Biological process     metabolic process   11 terms 
  Biochemical function     catalytic activity     6 terms  


DOI no: 10.1021/bi700083z Biochemistry 46:6277-6287 (2007)
PubMed id: 17474719  
Phosphorylation of serine 264 impedes active site accessibility in the E1 component of the human pyruvate dehydrogenase multienzyme complex.
F.Seifert, E.Ciszak, L.Korotchkina, R.Golbik, M.Spinka, P.Dominiak, S.Sidhu, J.Brauer, M.S.Patel, K.Tittmann.
At the junction of glycolysis and the Krebs cycle in cellular metabolism, the pyruvate dehydrogenase multienzyme complex (PDHc) catalyzes the oxidative decarboxylation of pyruvate to acetyl-CoA. In mammals, PDHc is tightly regulated by phosphorylation-dephosphorylation of three serine residues in the thiamin-dependent pyruvate dehydrogenase (E1) component. In vivo, inactivation of human PDHc correlates mostly with phosphorylation of serine 264, which is located at the entrance of the substrate channel leading to the active site of E1. Despite intense investigations, the molecular mechanism of this inactivation has remained enigmatic. Here, a detailed analysis of microscopic steps of catalysis in human wild-type PDHc-E1 and pseudophosphorylation variant Ser264Glu elucidates how phosphorylation of Ser264 affects catalysis. Whereas the intrinsic reactivity of the active site in catalysis of pyruvate decarboxylation remains nearly unaltered, the preceding binding of substrate to the enzyme's active site via the substrate channel and the subsequent reductive acetylation of the E2 component are severely slowed in the phosphorylation variant. The structure of pseudophosphorylation variant Ser264Glu determined by X-ray crystallography reveals no differences in the three-dimensional architecture of the phosphorylation loop or of the active site, when compared to those of the wild-type enzyme. However, the channel leading to the active site is partially obstructed by the side chain of residue 264 in the variant. By analogy, a similar obstruction of the substrate channel can be anticipated to result from a phosphorylation of Ser264. The kinetic and thermodynamic results in conjunction with the structure of Ser264Glu suggest that phosphorylation blocks access to the active site by imposing a steric and electrostatic barrier for substrate binding and active site coupling with the E2 component. As a Ser264Gln variant, which carries no charge at position 264, is also selectively deficient in pyruvate binding and reductive acetylation of E2, we conclude that mostly steric effects account for inhibition of PDHc by phosphorylation.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19240034 C.A.Brautigam, R.M.Wynn, J.L.Chuang, and D.T.Chuang (2009).
Subunit and catalytic component stoichiometries of an in vitro reconstituted human pyruvate dehydrogenase complex.
  J Biol Chem, 284, 13086-13098.  
19081061 M.Kato, R.M.Wynn, J.L.Chuang, S.C.Tso, M.Machius, J.Li, and D.T.Chuang (2008).
Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops.
  Structure, 16, 1849-1859.
PDB codes: 3exe 3exf 3exg 3exh 3exi
19081062 X.Y.Pei, C.M.Titman, R.A.Frank, F.J.Leeper, and B.F.Luisi (2008).
Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multienzyme complex.
  Structure, 16, 1860-1872.
PDB codes: 3duf 3dv0 3dva
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 codes are shown on the right.