PDBsum entry: 1qs0

Oxidoreductase

PDB id: 1qs0

Contents

Protein chains

407 a.a. *

338 a.a. *

Ligands

TDP

COI

Metals

_MG

Waters ×197

* Residue conservation analysis

PDB id:

1qs0

Name:

Oxidoreductase

Title:

Crystal structure of pseudomonas putida 2-oxoisovalerate deh (branched-chain alpha-keto acid dehydrogenase, e1b)

Structure:

2-oxoisovalerate dehydrogenase alpha-subunit. Chain: a. Engineered: yes. 2-oxoisovalerate dehydrogenase beta-subunit. Chain: b. Engineered: yes

Source:

Pseudomonas putida. Organism_taxid: 303. Expressed in: pseudomonas putida. Expression_system_taxid: 303.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.40Å R-factor: 0.218 R-free: 0.265

Authors:

A.Aevarsson,K.Seger,S.Turley,J.R.Sokatch,W.G.J.Hol

Key ref:

A.Aevarsson et al. (1999). Crystal structure of 2-oxoisovalerate and dehydrogenase and the architecture of 2-oxo acid dehydrogenase multienzyme complexes. Nat Struct Biol, 6, 785-792. PubMed id: 10426958 DOI: 10.1038/11563

Date:

24-Jun-99 Release date: 18-Aug-99

Protein chain

P09060  (ODBA_PSEPU) -  2-oxoisovalerate dehydrogenase subunit alpha

Seq: 410 a.a.

Struc: 407 a.a.

Protein chain

P09061  (ODBB_PSEPU) -  2-oxoisovalerate dehydrogenase subunit beta

Seq: 339 a.a.

Struc: 338 a.a.

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 = COI) matches with 60.00% 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 

• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (5 terms)

reference

DOI no: 10.1038/11563

Nat Struct Biol 6:785-792 (1999)

PubMed id: 10426958

Crystal structure of 2-oxoisovalerate and dehydrogenase and the architecture of 2-oxo acid dehydrogenase multienzyme complexes.

A.Aevarsson, K.Seger, S.Turley, J.R.Sokatch, W.G.Hol.

ABSTRACT

The family of giant multienzyme complexes metabolizing pyruvate, 2-oxoglutarate, branched-chain 2-oxo acids or acetoin contains several of the largest and most sophisticated protein assemblies known, with molecular masses between 4 and 10 million Da. The principal enzyme components, E1, E2 and E3, are present in numerous copies and utilize multiple cofactors to catalyze a directed sequence of reactions via substrate channeling. The crystal structure of a heterotetrameric (alpha2beta2) E1, 2-oxoisovalerate dehydrogenase from Pseudomonas putida, reveals a tightly packed arrangement of the four subunits with the beta2-dimer held between the jaws of a 'vise' formed by the alpha2-dimer. A long hydrophobic channel, suitable to accommodate the E2 lipoyl-lysine arm, leads to the active site, which contains the cofactor thiamin diphosphate (ThDP) and an inhibitor-derived covalent modification of a histidine side chain. The E1 structure, together with previous structural information on E2 and E3, completes the picture of the shared architectural features of these enormous macromolecular assemblies.

Selected figure(s)

Figure 3.
Figure 3. Structural organization of the heterotetrameric P. putida E1 [2] [2]. The diagram illustrates how the four subunits ( , ', and ') shown in each corner panel (i, g, a, c) associate into two separate dimers (b, h) and further into the [2] [2]-tetramer shown at the center (e). The secondary-structure elements (arrows for -strands, cylinders for -helices) and the location of the bound ThDP cofactor (space-filling) are shown for the -subunit (i), the '-subunit (c) and the [2] [2]-tetramer (f). Each subunit makes extensive surface contacts with the other three subunits, as illustrated in (a) and (g) by colored patches representing atoms within 5 Å from the same-colored subunit. Thus, in (a), yellow represents the contact surface of with ', blue the contact surface of with ', purple the contact surface of with . The [2]-dimer ( b) is tightly associated with the [2]-dimer (h) to form the assembled [2] [2]-tetramer ( e) with the jaws of the [2]-'vise' (h) firmly holding the [2]-dimer (b). The route of assembly implied in this diagram is purely illustrative and not supposed to represent assembly of the tetramer particle in vivo. d, Part of the '-subunit, with the side chains of nine selenomethionine residues (out of 22 in the asymmetric unit) together with a chicken-wire representation of a dispersive difference Fourier map (contoured at 3 ) used in the MAD structure determination (Table 2).

Figure 5.
Figure 5. The lipoyl-lysine arm of the E2 lipoyl domain visiting the active site of P. putida E1b. The modeled scene represents the interaction of the lipoyl domain with E1 just before the reductive acylation of the lipoamide catalyzed by E1. The E1 structure is shown as a solid that has been sliced in order to disclose the channel leading to the active site, at the interface between the -subunit and the '-subunit. The side chains of the active site histidinyl residues are shown explicitly. Also shown are a model of the enamine intermediate with the acyl group of the substrate at the C2 position of the ThDP cofactor, and a model of the incoming lipoyl domain with the lipoyl-lysine arm occupying the active site channel. The approximate 'viewpoint' of the lipoyl-lysine arm as it enters the active site channel can be seen in stereo in Fig. 4b. Either of the histidine residues (His 312 and His 131 ') is likely to be involved in the catalytic mechanism, possibly playing the role of a proton donor in the reduction of the disulfide bond of the lipoamide.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 785-792) copyright 1999.

Figures were selected by an automated process.