PDBsum entry 4g2e

Oxidoreductase

PDB id: 4g2e

Contents

Protein chain

151 a.a.

Waters ×305

PDB id:

4g2e

Name:

Oxidoreductase

Title:

Crystal structure of a dimeric prxq from sulfolobus tokodaii

Structure:

Peroxiredoxin. Chain: a. Engineered: yes

Source:

Sulfolobus tokodaii. Organism_taxid: 273063. Strain: dsm 16993 / jcm 10545 / nbrc 100140 / 7. Gene: bcp4, stk_17850. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.40Å R-factor: 0.121 R-free: 0.149

Authors:

A.Perkins,M.C.Gretes,P.A.Karplus

Key ref:

A.Perkins et al. (2012). Mapping the active site helix-to-strand conversion of CxxxxC peroxiredoxin Q enzymes. Biochemistry, 51, 7638-7650. PubMed id: 22928725

Date:

11-Jul-12 Release date: 24-Oct-12

Protein chain

F9VNL8  (F9VNL8_SULTO) -  Peroxiredoxin from Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)

Seq: 155 a.a.

Struc: 151 a.a.

Enzyme reactions

• Enzyme class: E.C.1.11.1.15 - Transferred entry: 1.11.1.24, 1.11.1.25, 1.11.1.26, 1.11.1.27, 1.11.1.28
• Pathway: Peroxiredoxin
• Reaction: 2 R'-SH + ROOH = R'-S-S-R' + H₂O + ROH

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

reference

Biochemistry 51:7638-7650 (2012)

PubMed id: 22928725

Mapping the active site helix-to-strand conversion of CxxxxC peroxiredoxin Q enzymes.

A.Perkins, M.C.Gretes, K.J.Nelson, L.B.Poole, P.A.Karplus.

ABSTRACT

Peroxiredoxins (Prx) make up a family of enzymes that reduce peroxides using a peroxidatic cysteine residue; among these, members of the PrxQ subfamily are proposed to be the most ancestral-like yet are among the least characterized. In many PrxQ enzymes, a second "resolving" cysteine is located five residues downstream from the peroxidatic Cys, and these residues form a disulfide during the catalytic cycle. Here, we describe three hyperthermophilic PrxQ crystal structures originally determined by the RIKEN structural genomics group. We reprocessed the diffraction data and conducted further refinement to yield models with R(free) values lowered by 2.3-7.2% and resolution extended by 0.2-0.3 Å, making one, at 1.4 Å, one of the best resolved peroxiredoxins to date. Comparisons of two matched thiol and disulfide forms reveal that the active site conformational change required for disulfide formation involves a transition of ∼20 residues from a pair of α-helices to a β-hairpin and 3(10)-helix. Each conformation has ∼10 residues with a high level of disorder providing slack that allows the dramatic shift, and the two conformations are anchored to the protein core by distinct nonpolar side chains that fill three hydrophobic pockets. Sequence conservation patterns confirm the importance of these and a few additional residues for function. From a broader perspective, this study raises the provocative question of how to make use of the valuable information in the Protein Data Bank generated by structural genomics projects but not described in the literature, perhaps remaining unrecognized and certainly underutilized.