PDBsum entry: 1x7z

Oxidoreductase

PDB id: 1x7z

Contents

Protein chains

391 a.a. *

329 a.a. *

Ligands

TDP

GOL

Metals

__K ×2

_MN

_CL

Waters ×636

* Residue conservation analysis

PDB id:

1x7z

Name:

Oxidoreductase

Title:

Crystal structure of the human mitochondrial branched-chain ketoacid dehydrogenase

Structure:

2-oxoisovalerate dehydrogenase alpha subunit. Chain: a. Synonym: branched-chain alpha-keto acid dehydrogenase e1 co alpha chain, bckdh e1-alpha, bckde1a. Engineered: yes. Mutation: yes. 2-oxoisovalerate dehydrogenase beta subunit. Chain: b. Synonym: branched-chain alpha-keto acid dehydrogenase e1 co

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: bckdha. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Gene: bckdhb.

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.72Å R-factor: 0.154 R-free: 0.189

Authors:

R.M.Wynn,M.Kato,M.Machius,J.L.Chuang,J.Li,D.R.Tomchick,D.T.C

Key ref:

R.M.Wynn et al. (2004). Molecular mechanism for regulation of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase complex by phosphorylation. Structure, 12, 2185-2196. PubMed id: 15576032 DOI: 10.1016/j.str.2004.09.013

Date:

16-Aug-04 Release date: 23-Nov-04

Protein chain

P12694  (ODBA_HUMAN) -  2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial

Seq: 445 a.a.

Struc: 391 a.a.*

Protein chain

P21953  (ODBB_HUMAN) -  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial

Seq: 392 a.a.

Struc: 329 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.1.2.4.4 - 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring).
• Pathway: Oxo-acid dehydrogenase complexes
• Reaction: 3-methyl-2-oxobutanoate + [dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] lipoyllysine = [dihydrolipoyllysine- residue (2-methylpropanoyl)transferase] S-(2-methylpropanoyl)dihydrolipoyllysine + CO₂

3-methyl-2-oxobutanoate (Bound ligand (Het Group name = GOL) matches with 55.56% similarity) + [dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] lipoyllysine = [dihydrolipoyllysine- residue (2-methylpropanoyl)transferase] S-(2-methylpropanoyl)dihydrolipoyllysine + CO(2)

• Cofactor: Thiamine diphosphate

Thiamine diphosphate (Bound ligand (Het Group name = TDP) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: mitochondrion (3 terms)
• Biological process: metabolic process (4 terms)
• Biochemical function: catalytic activity (8 terms)

reference

DOI no: 10.1016/j.str.2004.09.013

Structure 12:2185-2196 (2004)

PubMed id: 15576032

Molecular mechanism for regulation of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase complex by phosphorylation.

R.M.Wynn, M.Kato, M.Machius, J.L.Chuang, J.Li, D.R.Tomchick, D.T.Chuang.

ABSTRACT

The human mitochondrial branched-chain alpha-ketoacid dehydrogenase complex (BCKDC) is a 4 MDa macromolecular machine comprising three catalytic components (E1b, E2b, and E3), a kinase, and a phosphatase. The BCKDC overall activity is tightly regulated by phosphorylation in response to hormonal and dietary stimuli. We report that phosphorylation of Ser292-alpha in the E1b active site channel results in an order-to-disorder transition of the conserved phosphorylation loop carrying the phosphoryl serine. The conformational change is triggered by steric clashes of the phosphoryl group with invariant His291-alpha that serves as an indispensable anchor for the phosphorylation loop through bound thiamin diphosphate. Phosphorylation of Ser292-alpha does not severely impede the E1b-dependent decarboxylation of alpha-ketoacids. However, the disordered loop conformation prevents phosphorylated E1b from binding the E2b lipoyl-bearing domain, which effectively shuts off the E1b-catalyzed reductive acylation reaction and therefore completely inactivates BCKDC. This mechanism provides a paradigm for regulation of mitochondrial alpha-ketoacid dehydrogenase complexes by phosphorylation.

Selected figure(s)

Figure 6.
Figure 6. Predicted Steric Clashes in Phosphorylated, S292E-a, and S292Q-a E1b Structures(A-D) In the (A) phosphorylated, (B) S292E-a, (C) S292N-a, and (D) S292Q-a structures, modeled van der Waals surfaces for the phosphoryl group or substituted residues, which predict steric clashes with His291-a, except Asn292-a, are based on coordinates of the wild-type structure in Figure 5A. These steric clashes result in the destabilization of the hydrogen bond network and therefore disorder the loop. Conformations for ThDP, Arg114-a, and the Cl - ion that coordinates to the 4' amino group on the aminopyrimidine ring of ThDP, His146-b', and Tyr113-a are derived from 2F[o] - F[c] electron densities.

The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 2185-2196) copyright 2004.

Figure was selected by the author.