PDBsum entry 2bfb

Oxidoreductase

PDB id: 2bfb

Contents

Protein chains

370 a.a. *

329 a.a. *

Ligands

TPP

GOL

MRD

Metals

_CL ×2

__K ×2

_MN

Waters ×644

* Residue conservation analysis

PDB id:

2bfb

Name:

Oxidoreductase

Title:

Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch

Structure:

2-oxoisovalerate dehydrogenase alpha subunit. Chain: a. Fragment: residues 46-445. Synonym: branched-chain alpha-keto acid dehydrogenase e1 component alpha chain, bckdh e1-alpha, bckde1a. Engineered: yes. Mutation: yes. 2-oxoisovalerate dehydrogenase beta subunit. Chain: b.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Groes.

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.77Å R-factor: 0.145 R-free: 0.184

Authors:

M.Machius,R.M.Wynn,J.L.Chuang,D.R.Tomchick,C.A.Brautigam,D.T.Chuang

Key ref:

M.Machius et al. (2006). A versatile conformational switch regulates reactivity in human branched-chain alpha-ketoacid dehydrogenase. Structure, 14, 287-298. PubMed id: 16472748 DOI: 10.1016/j.str.2005.10.009

Date:

06-Dec-04 Release date: 16-Feb-06

Protein chain

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

Seq: 445 a.a.

Struc: 370 a.a.*

Protein chain

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

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: N₆-[(R)-lipoyl]-L-lysyl-[protein] + 3-methyl-2-oxobutanoate + H⁺ = N₆-[(R)-S(8)-2-methylpropanoyldihydrolipoyl]-L-lysyl-[protein] + CO2

N(6)-[(R)-lipoyl]-L-lysyl-[protein] + 3-methyl-2-oxobutanoate (Bound ligand (Het Group name = MRD) matches with 60.00% similarity) + H(+) = N(6)-[(R)-S(8)-2-methylpropanoyldihydrolipoyl]-L-lysyl-[protein] + CO2

• 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

reference

DOI no: 10.1016/j.str.2005.10.009

Structure 14:287-298 (2006)

PubMed id: 16472748

A versatile conformational switch regulates reactivity in human branched-chain alpha-ketoacid dehydrogenase.

M.Machius, R.M.Wynn, J.L.Chuang, J.Li, R.Kluger, D.Yu, D.R.Tomchick, C.A.Brautigam, D.T.Chuang.

ABSTRACT

The dehydrogenase/decarboxylase (E1b) component of the 4 MD human branched-chain alpha-ketoacid dehydrogenase complex (BCKDC) is a thiamin diphosphate (ThDP)-dependent enzyme. We have determined the crystal structures of E1b with ThDP bound intermediates after decarboxylation of alpha-ketoacids. We show that a key tyrosine residue in the E1b active site functions as a conformational switch to reduce the reactivity of the ThDP cofactor through interactions with its thiazolium ring. The intermediates do not assume the often-postulated enamine state, but likely a carbanion state. The carbanion presumably facilitates the second E1b-catalyzed reaction, involving the transfer of an acyl moiety from the intermediate to a lipoic acid prosthetic group in the transacylase (E2b) component of the BCKDC. The tyrosine switch further remodels an E1b loop region to promote E1b binding to E2b. Our results illustrate the versatility of the tyrosine switch in coordinating the catalytic events in E1b by modulating the reactivity of reaction intermediates.

Selected figure(s)

Figure 8.
Figure 8. Scheme of hE1b-Catalyzed Reactions Emphasizing the Role of Tyr113-a as the Central Regulatory Conformational Switch
(A) Prior to substrate binding, the side chain of Tyr113-a, the switch turn (indicated by Q112|Y113|R114), and the adjacent LBD binding region are in the S conformation.
(B) Substrate binding displaces the Tyr113-a side chain and forces it into the P conformation, where it establishes a hydrogen bond to the terminal phosphate group in the ThDP cofactor and additional interactions with the sulfur in the thiazolium ring (dashed lines). Simultaneously, the switch turn is remodeled, whereupon the adjacent LBD binding region adopts a higher-affinity state for LBD.
(C and D) After, or concomitant with, (C) decarboxylation, LBD binds to hE1b, followed by (D) the transfer of an acyl moiety, derived from the degradation of valine, leucine, or isoleucine to lipoic acid (LA).
TZ, thiazolium ring; AP, aminopyrimidine ring; B, general base.

The above figure is reprinted by permission from Cell Press: Structure (2006, 14, 287-298) copyright 2006.

Figure was selected by an automated process.