PDBsum entry: 2c3o

Oxidoreductase

PDB-id: 2c3o

Biological unit = asymmetric unit,
as shown
(as defined in PDB file)

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

1231 a.a. *

Ligands

SF4 ×6

TPP ×2

PYR ×2

Metal ions

_MG ×2

_CA ×2

Waters ×569

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

2c3o

Name:

Oxidoreductase

Title:

Crystal structure of the free radical intermediate 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 15 minutes with pyruvate

Source:

Desulfovibrio africanus. Organism_taxid: 873

Biological unit:

Dimer (from PDB file)

UniProt:

Chains A, B: P94692 (P94692_DESAF)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

1232 a.a.

Struc:

1231 a.a.

Key:	PfamA domain	PfamB domain
Secondary structure	CATH domain

Resolution:

2.7Å

R-factor:

0.205

R-free:

0.268

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:

11-Oct-05

Release date:

15-Feb-06

Related entries:

1b0p crystal structure of pyruvate-ferredoxin oxidoreductase from desulfovibrio africanus
1kek crystal structure of the free radical intermediate ofpyruvate:ferredoxin oxidoreductase
2c3m crystal structure of pyruvate-ferredoxin oxidoreductase from desulfovibrio africanus
2c3p crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase from desulfovibrio africanus
2c3u crystal structure of pyruvate-ferredoxin oxidoreductase from desulfovibrio africanus, oxygen inhibited form
2c3y crystal structure of the radical form of pyruvate:ferredoxin oxidoreductase from desulfovibrio africanus
2c42 crystal structure of pyruvate-ferredoxin oxidoreductase from desulfovibrio africanus
2pda crystal structure of the complex between pyruvate- ferredoxin oxidoreductase from desulfovibrio africanus and pyruvate.

Quick_links

Procheck

Surface

Key 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.