PDBsum entry: 2a4v

Oxidoreductase

PDB id: 2a4v

Contents

Protein chain

156 a.a. *

Waters ×156

* Residue conservation analysis

PDB id:

2a4v

Name:

Oxidoreductase

Title:

Crystal structure of a truncated mutant of yeast nuclear thiol peroxidase

Structure:

Peroxiredoxin dot5. Chain: a. Fragment: c-terminal domain. Synonym: thioredoxin reductase, nuclear thiol peroxidase, ntpx, disrupter of telomere silencing protein 5. Engineered: yes. Mutation: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: dot5. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.80Å R-factor: 0.167 R-free: 0.215

Authors:

J.Choi,S.Choi,J.-K.Chon,J.Choi,M.-K.Cha,I.-H.Kim,W.Shin

Key ref:

J.Choi et al. (2005). Crystal structure of the C107S/C112S mutant of yeast nuclear 2-Cys peroxiredoxin. Proteins, 61, 1146-1149. PubMed id: 16245326 DOI: 10.1002/prot.20704

Date:

29-Jun-05 Release date: 14-Mar-06

Protein chain

P40553  (DOT5_YEAST) -  Peroxiredoxin DOT5

Seq: 215 a.a.

Struc: 156 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.11.1.15 - Peroxiredoxin.
• 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

 Gene Ontology (GO) functional annotation 

• Biological process: oxidation-reduction process (1 term)
• Biochemical function: antioxidant activity (2 terms)

reference

DOI no: 10.1002/prot.20704

Proteins 61:1146-1149 (2005)

PubMed id: 16245326

Crystal structure of the C107S/C112S mutant of yeast nuclear 2-Cys peroxiredoxin.

J.Choi, S.Choi, J.K.Chon, J.Choi, M.K.Cha, I.H.Kim, W.Shin.

ABSTRACT

Selected figure(s)

Figure 1.
Figure 1. A: Ribbon diagram of tmTPx. -Helices and -strands are colored orange and cyan, respectively. Absolutely conserved residues are represented by stick models, with carbon in green, oxygen in red, and nitrogen in blue. Ser107 and Ser112 are labeled as C[P] and C[R], and their O atoms are depicted as spheres in orange and blue, respectively. B: Structure-based sequence alignment of selected Prxs. Human PrxVI was selected as a representative for 1-Cys Prxs, S. typhimurium Ahpc for T2-Cys (typical 2-Cys Prxs), S. pneumoniae TPx for L2-Cys (L-type atypical 2-Cys Prxs), human PrxV for R2-Cys (R-type atypical 2-Cys Prxs), and yeast nTPx for C2-Cys (C-type atypical 2-Cys Prxs). The residues involved in -strands, -helices, and 3[10]-helices are shaded with cyan, yellow, and light brown, respectively. The secondary structure elements have been labeled based on the labeling of tmTPx. C[P] in parenthesis denotes the position of the C[P] residue common to all Prxs, and C, L, R, and T in parentheses denote the positions of the C[R] residues of T2-Cys, L2-Cys, R2-Cys, and C2-Cys Prxs, respectively. Four residues that are absolutely conserved in all Prxs are colored red, and the C[R] residues are colored blue on red. For the C2-Cys, only a part of the residues, truncated in tmTPx, are shown shaded with light gray and the 48 N-terminal sequences of yeast nTPx were omitted. C: Comparison of the Prx structures representing each subfamily. C -traces are shown in yellow for human PrxVI (PDB code, 1prx), purple for S. typhimurium Ahpc (1n8j), green for S. pneumoniae TPx (1psq), red for human PrxV (1h4o), and blue for yeast tmTPx (thick line). The structures were superposed using the atoms in the -sheets. Colored spheres labeled as C[P], T, L, R, and C denote the catalytic Cys residues, as described in B. S denotes the putative substrate-binding site, and 4- 6 and 7- 5 denote the loops connecting the corresponding secondary structure elements.

The above figure is reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 61, 1146-1149) copyright 2005.