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

References listed in PDB file

Key reference

Title

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

Authors

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

Ref.

Nat Struct Biol, 1999, 6, 182-190. [DOI no: 10.1038/5870]

PubMed id

10048931

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.

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.

Secondary reference #1

Title

Crystallization and preliminary crystallographic analysis of the pyruvate-Ferredoxin oxidoreductase from desulfovibrio africanus.

Authors

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

Ref.

Acta Crystallogr D Biol Crystallogr, 1999, 55, 329-331. [DOI no: 10.1107/S0907444998008920]

PubMed id

10089441

Figure 1.
Figure 1 Orthorhombic crystal of pyruvate-ferredoxin oxidoreductase from D. africanus. The crystal is approximately 0.3 × 0.3 × 0.4 mm.

The above figure is reproduced from the cited reference with permission from the IUCr