PDBsum entry 3dv0

Oxidoreductase/transferase

PDB id: 3dv0

Contents

Protein chains

349 a.a. *

324 a.a. *

43 a.a. *

Ligands

TPW ×4

PYR ×2

Metals

_MG ×6

__K ×4

Waters ×990

* Residue conservation analysis

PDB id:

3dv0

Name:

Oxidoreductase/transferase

Title:

Snapshots of catalysis in the e1 subunit of the pyruvate dehydrogenase multi-enzyme complex

Structure:

Pyruvate dehydrogenase e1 component subunit alpha. Chain: a, c, e, g. Engineered: yes. Pyruvate dehydrogenase e1 component subunit beta. Chain: b, d, f, h. Engineered: yes. Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex. Chain: i, j.

Source:

Bacillus stearothermophilus. Gene: pdha. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: pdhb. Gene: pdhc.

Resolution:

2.50Å R-factor: 0.176 R-free: 0.241

Authors:

X.Y.Pei,C.M.Titman,R.A.W.Frank,F.J.Leeper,B.F.Luisi

Key ref:

X.Y.Pei et al. (2008). Snapshots of catalysis in the e1 subunit of the pyruvate dehydrogenase multienzyme complex. Structure, 16, 1860-1872. PubMed id: 19081062 DOI: 10.1016/j.str.2008.10.009

Date:

18-Jul-08 Release date: 13-Jan-09

Protein chains

P21873  (ODPA_GEOSE) -  Pyruvate dehydrogenase E1 component subunit alpha from Geobacillus stearothermophilus

Seq: 369 a.a.

Struc: 349 a.a.

Protein chains

P21874  (ODPB_GEOSE) -  Pyruvate dehydrogenase E1 component subunit beta from Geobacillus stearothermophilus

Seq: 325 a.a.

Struc: 324 a.a.

Protein chains

P11961  (ODP2_GEOSE) -  Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex from Geobacillus stearothermophilus

Seq: 428 a.a.

Struc: 43 a.a.

Enzyme reactions

• Enzyme class 1: Chains A, B, C, D, E, F, G, H: E.C.1.2.4.1 - pyruvate dehydrogenase (acetyl-transferring).
• Pathway: Oxo-acid dehydrogenase complexes
• Reaction: N₆-[(R)-lipoyl]-L-lysyl-[protein] + pyruvate + H⁺ = N₆-[(R)-S(8)- acetyldihydrolipoyl]-L-lysyl-[protein] + CO2

N(6)-[(R)-lipoyl]-L-lysyl-[protein] + pyruvate + H(+) (Bound ligand (Het Group name = PYR) corresponds exactly) = N(6)-[(R)-S(8)- acetyldihydrolipoyl]-L-lysyl-[protein] + CO2

• Cofactor: Thiamine diphosphate

Thiamine diphosphate (Bound ligand (Het Group name = TPW) matches with 44.44% similarity)

• Enzyme class 2: Chains I, J: E.C.2.3.1.12 - dihydrolipoyllysine-residue acetyltransferase.

Pathway:

• Reaction: N₆-[(R)-dihydrolipoyl]-L-lysyl-[protein] + acetyl-CoA = N₆-[(R)-S(8)- acetyldihydrolipoyl]-L-lysyl-[protein] + CoA

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1016/j.str.2008.10.009

Structure 16:1860-1872 (2008)

PubMed id: 19081062

Snapshots of catalysis in the e1 subunit of the pyruvate dehydrogenase multienzyme complex.

X.Y.Pei, C.M.Titman, R.A.Frank, F.J.Leeper, B.F.Luisi.

ABSTRACT

The pyruvate dehydrogenase multienzyme assembly (PDH) generates acetyl coenzyme A and reducing equivalents from pyruvate in a multiple-step process that is a nexus of central metabolism. We report crystal structures of the Geobacillus stearothermophilus PDH E1p subunit with ligands that mimic the prereaction complex and the postdecarboxylation product. The structures implicate residues that help to orient substrates, nurture intermediates, and organize surface loops so that they can engage a mobile lipoyl domain that receives the acetyl group and shuttles it to the next active site. The structural and enzymatic data suggest that H128beta performs a dual role: first, as electrostatic catalyst of the reaction of pyruvate with the thiamine cofactor; and second, as a proton donor in the second reaction of acetyl group with the lipoate. We also identify I206alpha as a key residue in mediating the conformation of active-site loops. We propose that a simple conformational flip of the H271alpha side chain assists transfer of the acetyl group from thiamine cofactor to lipoyl domain in synchrony with reduction of the dithiolane ring.

Selected figure(s)

Figure 5.
Figure 5. Hydration Patterns in the Active-Site Pocket Near the ThDP Cofactor
The substitution of the bulky isoleucine by alanine in the I206Aα mutant changes the hydration pattern around the cofactor. The wild-type structure (green) is overlayed with the mutant in complex with 3-deazaThDP (cyan).

Figure 6.
Figure 6. Postulated Path of the Lipoate in the E1 Active Site
(A) Hydration pattern along the pathway to the active site. The enzyme exterior is on the right in this view.
(B) Hydration pattern in the lipoate path in the he-3-deazaThDP complex. The red spheres represent the water molecules.
(C) Model of the docked oxidised lipoate. The access channel is shown as a section through a space-filling surface. The cofactor, lipoyl-lysine, and a portion of the lipoyl domain peptide backbone are shown.
(D) A speculative model showing how the dithiolane ring might be presented to the active-site pocket residues in E1p. A simple 180° flip about the Cγ–Cβ bond brings the H271αN epsilon away from close contact with the thiazole S and orientated toward the thiolane ring of the oxidised ring. This could orchestrate electronic perturbations of the thiazole and dithiolane rings that facilitate the reductive acylation.

The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 1860-1872) copyright 2008.

Figures were selected by an automated process.