1w85 Summary

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THE CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE E1 BOUND TO THE PERIPHERAL SUBUNIT BINDING DOMAIN OF E2

The structure was published by Frank, R.A.W., Titman, C.M., Pratap, J.V., Luisi, B.F., and Perham, R.N., in 2004 in a paper entitled "A Molecular Switch and Proton Wire Synchronize the Active Sites in Thiamine Enzymes" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.0 Å and deposited in 2004.

The experimental data on which the structure is based was also deposited.

This PDB entry contains a complex of 3 biomacromolecules, namely PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT, PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT, and DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule has more than one probable quaternary state observed. For more details see the quaternary structure page.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT P21873 (2-369) (ODPA_GEOSE)search Geobacillus stearothermophilussearch 100% 368 99%
C PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT P21873 (2-369) (ODPA_GEOSE)search Geobacillus stearothermophilussearch 100% 368 99%
E PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT P21873 (2-369) (ODPA_GEOSE)search Geobacillus stearothermophilussearch 100% 368 99%
G PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT P21873 (2-369) (ODPA_GEOSE)search Geobacillus stearothermophilussearch 100% 368 99%
B PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT P21874 (2-325) (ODPB_GEOSE)search Geobacillus stearothermophilussearch 100% 324 100%
D PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT P21874 (2-325) (ODPB_GEOSE)search Geobacillus stearothermophilussearch 100% 324 100%
F PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT P21874 (2-325) (ODPB_GEOSE)search Geobacillus stearothermophilussearch 100% 324 100%
H PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT P21874 (2-325) (ODPB_GEOSE)search Geobacillus stearothermophilussearch 100% 324 100%
I DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE P11961 (123-171) (ODP2_GEOSE)search Geobacillus stearothermophilussearch 100% 49 85%
J DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE P11961 (123-171) (ODP2_GEOSE)search Geobacillus stearothermophilussearch 100% 49 85%


This entry contains 3 unique UniProt proteins:

UniProt accession Name Organism PDB
P21873 (2 - 369) PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT Geobacillus stearothermophilus
P21874 (2 - 325) PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT Geobacillus stearothermophilus
P11961 (123 - 171) DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE Geobacillus stearothermophilus

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A, C, E, G (P21873) Branched-chain alpha-keto acid dehydrogenase PP modulesearch Rossmann foldsearch PF00676: Dehydrogenase E1 componentsearch
B, D, F, H (P21874) Branched-chain alpha-keto acid dehydrogenase Pyr modulesearch, Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domainsearch Rossmann foldsearch PF02779: Transketolase, pyrimidine binding domainsearch, PF02780: Transketolase, C-terminal domainsearch
I, J (P11961) Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complexsearch Dihydrolipoamide Transferasesearch PF02817: e3 binding domainsearch

Chain ID Biological process (GO) Molecular function (GO)
A, C, E, G (P21873) glycolytic processsearch oxidation-reduction processsearch metabolic processsearch pyruvate dehydrogenase (acetyl-transferring) activitysearch oxidoreductase activitysearch oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptorsearch
B, D, F, H (P21874) metabolic processsearch glycolytic processsearch oxidation-reduction processsearch pyruvate dehydrogenase (acetyl-transferring) activitysearch catalytic activitysearch oxidoreductase activitysearch
I, J (P11961) metabolic processsearch transferase activity, transferring acyl groupssearch

Chain InterPro annotation
A, C, E, G Dehydrogenase, E1 componentsearch Pyruvate dehydrogenase E1 component subunit alpha/BCKADH E1-alphasearch Thiamin diphosphate-binding foldsearch
B, D, F, H Transketolase-like, pyrimidine-binding domainsearch Transketolase, C-terminalsearch Transketolase, C-terminal/Pyruvate-ferredoxin oxidoreductase, domain IIsearch Thiamin diphosphate-binding foldsearch
I, J E3 bindingsearch