PDBsum entry 2c3y

Oxidoreductase

PDB id: 2c3y

Contents

Protein chains

1231 a.a. *

Ligands

SF4 ×6

HTL ×2

CO2 ×2

Metals

_MG ×2

_CA ×2

Waters ×1978

* Residue conservation analysis

PDB id:

2c3y

Name:

Oxidoreductase

Title:

Crystal structure of the radical form of pyruvate:ferredoxin oxidoreductase from desulfovibrio africanus

Structure:

Pyruvate-ferredoxin oxidoreductase. Chain: a, b. Other_details: complexed with iron/sulfur cluster, thiamin diphosphate, crystal soaked overnight with pyruvate

Source:

Desulfovibrio africanus. Organism_taxid: 873

Biol. unit:

Dimer (from PDB file)

Resolution:

1.93Å R-factor: 0.186 R-free: 0.228

Authors:

C.Cavazza,C.Contreras-Martel,L.Pieulle,E.Chabriere,E.C.Hatchikian, J.C.Fontecilla-Camps

Key ref:

C.Cavazza et al. (2006). Flexibility of thiamine diphosphate revealed by kinetic crystallographic studies of the reaction of pyruvate-ferredoxin oxidoreductase with pyruvate. Structure, 14, 217-224. PubMed id: 16472741 DOI: 10.1016/j.str.2005.10.013

Date:

13-Oct-05 Release date: 15-Feb-06

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

• Cofactor: Iron-sulfur; Thiamine diphosphate

Iron-sulfur Thiamine diphosphate (Bound ligand (Het Group name = HTL) matches with 89.66% similarity)

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

reference

DOI no: 10.1016/j.str.2005.10.013

Structure 14:217-224 (2006)

PubMed id: 16472741

Flexibility of thiamine diphosphate revealed by kinetic crystallographic studies of the reaction of pyruvate-ferredoxin oxidoreductase with pyruvate.

C.Cavazza, C.Contreras-Martel, L.Pieulle, E.Chabrière, E.C.Hatchikian, J.C.Fontecilla-Camps.

ABSTRACT

Pyruvate-ferredoxin oxidoreductases (PFOR) are unique among thiamine pyrophosphate (ThDP)-containing enzymes in giving rise to a rather stable cofactor-based free-radical species upon the decarboxylation of their first substrate, pyruvate. We have obtained snapshots of unreacted and partially reacted (probably as a tetrahedral intermediate) pyruvate-PFOR complexes at different time intervals. We conclude that pyruvate decarboxylation involves very limited substrate-to-product movements but a significant displacement of the thiazolium moiety of ThDP. In this respect, PFOR seems to differ substantially from other ThDP-containing enzymes, such as transketolase and pyruvate decarboxylase. In addition, exposure of PFOR to oxygen in the presence of pyruvate results in significant inhibition of catalytic activity, both in solution and in the crystals. Examination of the crystal structure of inhibited PFOR suggests that the loss of activity results from oxime formation at the 4' amino substituent of the pyrimidine moiety of ThDP.

Selected figure(s)

Figure 2.
Figure 2. Electron Density Map of Oxygen-Inhibited PFOR
Pyruvate was excluded from phase and structure factor calculations (omit map). The electron density peak next to N4' of the aminopyrimidine ring may represent the oxygen atom of an oxime moiety. This and the displacement of a water molecule are the only differences between inhibited and active PFORs (see Figure 3A). This figure and Figure 3 and Figure 6 were prepared with TURBO (Roussel and Cambillaud, 1989).

The above figure is reprinted by permission from Cell Press: Structure (2006, 14, 217-224) copyright 2006.

Figure was selected by an automated process.