PDBsum entry 2pda

Oxidoreductase

PDB id: 2pda

Contents

Protein chains

1231 a.a. *

Ligands

SF4 ×6

TPP ×2

PYR ×2

Metals

_MG ×2

_CA ×2

Waters ×14

* Residue conservation analysis

PDB id:

2pda

Name:

Oxidoreductase

Title:

Crystal structure of the complex between pyruvate-ferredoxin oxidoreductase from desulfovibrio africanus and pyruvate.

Structure:

Protein (pyruvate-ferredoxin oxidoreductase). Chain: a, b. Other_details: complexed with iron/sulfur cluster, thiamin diphosphate, pyruvic acid

Source:

Desulfovibrio africanus. Organism_taxid: 873. Strain: ncib 8401. Cellular_location: cytoplasm

Biol. unit:

Dimer (from PQS)

Resolution:

3.00Å R-factor: 0.234 R-free: 0.297

Authors:

E.Chabriere,M.H.Charon

Key ref:

E.Chabrière et al. (1999). Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate. Nat Struct Biol, 6, 182-190. PubMed id: 10048931 DOI: 10.1038/5870

Date:

10-Nov-98 Release date: 23-Apr-99

Protein chains

P94692  (PFOR_DESAF) -  Pyruvate:ferredoxin oxidoreductase from Desulfocurvibacter africanus

Seq: 1232 a.a.

Struc: 1231 a.a.

Enzyme reactions

• Enzyme class: E.C.1.2.7.1 - pyruvate synthase.
• Reaction: 2 oxidized [2Fe-2S]-[ferredoxin] + pyruvate + CoA = 2 reduced [2Fe-2S]- [ferredoxin] + acetyl-CoA + CO2 + H⁺

2 × oxidized [2Fe-2S]-[ferredoxin] + pyruvate + CoA (Bound ligand (Het Group name = PYR) corresponds exactly) = 2 × reduced [2Fe-2S]- [ferredoxin] + acetyl-CoA + CO2 + H(+)

• Cofactor: Iron-sulfur; Thiamine diphosphate

Iron-sulfur 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: 10.1038/5870

Nat Struct Biol 6:182-190 (1999)

PubMed id: 10048931

Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate.

E.Chabrière, M.H.Charon, A.Volbeda, L.Pieulle, E.C.Hatchikian, J.C.Fontecilla-Camps.

ABSTRACT

Oxidative decarboxylation of pyruvate to form acetyl-coenzyme A, a crucial step in many metabolic pathways, is carried out in most aerobic organisms by the multienzyme complex pyruvate dehydrogenase. In most anaerobes, the same reaction is usually catalyzed by a single enzyme, pyruvate:ferredoxin oxidoreductase (PFOR). Thus, PFOR is a potential target for drug design against certain anaerobic pathogens. Here, we report the crystal structures of the homodimeric Desulfovibrio africanus PFOR (data to 2.3 A resolution), and of its complex with pyruvate (3.0 A resolution). The structures show that each subunit consists of seven domains, one of which affords protection against oxygen. The thiamin pyrophosphate (TPP) cofactor and the three [4Fe-4S] clusters are suitably arranged to provide a plausible electron transfer pathway. In addition, the PFOR-pyruvate complex structure shows the noncovalent fixation of the substrate before the catalytic reaction.

Selected figure(s)

Figure 1.
Figure 1. Ribbon drawings of Desulfovibrio africanus PFOR, made with MOLSCRIPT^48 and Raster3D^49. a,b, Two perpendicular views. Subunits are shown in light blue and dark blue. TPP cofactors are highlighted in bright red, Mg ions in green, iron atoms in brown and sulfur atoms in yellow.

Figure 3.
Figure 3. Ribbon drawings of the seven structural domains of Desulfovibrio africanus PFOR. In the included topology diagrams, −helices are represented by circles and −strands by triangles. A common folding motif in the core domains I, II and VI is indicated by the dots in their topology diagrams. For clarity, domains and topology diagrams are not represented in the same orientation.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 182-190) copyright 1999.

Figures were selected by an automated process.