PDBsum entry: 3duf

Oxidoreductase/transferase

PDB-id: 3duf

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Description

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Header records

References

PROCHECK

Protein chains

365 a.a. *

324 a.a. *

38 a.a. *

36 a.a. *

Ligands

R1T ×4

Metal ions

_MG ×5

__K ×2

Waters ×407

* Residue conservation analysis

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Clefts Calculation

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PDB id:

3duf

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.

Source:

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

UniProt:

Chains A, C, E, G: P21873 (ODPA_BACST)

Seq:
Struc:
	Seq:	369 a.a.
	Struc:	365 a.a.

Chains B, D, F, H: P21874 (ODPB_BACST)

Seq:
Struc:
	Seq:	325 a.a.
	Struc:	324 a.a.

Chain I: P11961 (ODP2_BACST)

Seq:
Struc:
	Seq:	428 a.a.
	Struc:	38 a.a.

Chain J: P11961 (ODP2_BACST)

Seq:

Struc:

Seq:

428 a.a.

Struc:

36 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class 1:

Chains A, B, C, D, E, F, G, H: E.C.1.2.4.1   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Pyruvate + [dihydrolipoyllysine-residue acetyltransferase] lipoyllysine = [dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine + CO₂ (see diagram below)

Cofactor:

Thiamine diphosphate

Pathway:

Oxo-acid dehydrogenase complexes

Enzyme class 2:

Chains I, J: E.C.2.3.1.12   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Acetyl-CoA + enzyme N₆-(dihydrolipoyl)lysine = CoA + enzyme N₆-(S-acetyldihydrolipoyl)lysine (see diagram below)

Pathway:

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.

Resolution:

2.50Å

R-factor:

0.192

R-free:

0.263

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:

17-Jul-08

Release date:

06-Jan-09

Related entries:

1w85
protein with different co-factor
1w88
protein with different co-factor
3dv0
3dva

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Key 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 the author.