PDBsum entry 1x0r

Oxidoreductase

PDB id: 1x0r

Contents

Protein chains

(+ 4 more) 244 a.a. *

Ligands

EDO ×128

Waters ×1189

* Residue conservation analysis

PDB id:

1x0r

Name:

Oxidoreductase

Title:

Thioredoxin peroxidase from aeropyrum pernix k1

Structure:

Probable peroxiredoxin. Chain: a, b, c, d, e, f, g, h, i, j. Synonym: thioredoxin peroxidase. Engineered: yes. Mutation: yes

Source:

Aeropyrum pernix. Organism_taxid: 272557. Strain: k1. Gene: ape2278. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Decamer (from PQS)

Resolution:

2.00Å R-factor: 0.164 R-free: 0.171

Authors:

T.Nakamura,T.Yamamoto,T.Inoue,H.Matsumura,A.Kobayashi,Y.Hagihara, K.Uegaki,M.Ataka,Y.Kai,K.Ishikawa

Key ref:

T.Nakamura et al. (2006). Crystal structure of thioredoxin peroxidase from aerobic hyperthermophilic archaeon Aeropyrum pernix K1. Proteins, 62, 822-826. PubMed id: 16342268 DOI: 10.1002/prot.20796

Date:

28-Mar-05 Release date: 20-Dec-05

Protein chains

Q9Y9L0  (TDXH_AERPE) -  Peroxiredoxin from Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)

Seq: 250 a.a.

Struc: 244 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.11.1.24 - thioredoxin-dependent peroxiredoxin.
• Reaction: a hydroperoxide + [thioredoxin]-dithiol = an alcohol + [thioredoxin]- disulfide + H2O

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

Added reference

DOI no: 10.1002/prot.20796

Proteins 62:822-826 (2006)

PubMed id: 16342268

Crystal structure of thioredoxin peroxidase from aerobic hyperthermophilic archaeon Aeropyrum pernix K1.

T.Nakamura, T.Yamamoto, T.Inoue, H.Matsumura, A.Kobayashi, Y.Hagihara, K.Uegaki, M.Ataka, Y.Kai, K.Ishikawa.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. Representation of the tertiary structure. a: The monomer structure of SeC207S is drawn. The side chains of Cys50, Ser207, and Cys213 are represented as balls and sticks. b: The dimer structure. The dark green subunit is in the same orientation as in (a). The arrow indicates the antiparallel -sheet formed by the 1 strands of the subunits. c: The dimer structure from the perpendicular direction as to in (b). The top and bottom views are from opposite directions to each other. The circles indicate the arm domains, which stick out of the main body of the dimer (see text). The side chains of Cys50, Ser207, and Cys213 are represented as balls and sticks in (a), (b), and (c). d: The decamer structure from the same direction as in (a). The names of the subunits are indicated. The outer and inner diameters of the ring are indicated by double-headed arrows. e: Two homodimers (AB and IJ) are presented from the direction indicated by an open arrow in (d). The positions of the AM interactions and the MM interaction are indicated by red circles and a yellow square, respectively. f: Close-up of the interface of the AM interaction indicated by the upper circle in panel (e). The hydrogen bond networks involving Thr191, Glu193, Asp209 are depicted.

Figure 2.
Figure 2. Comparison with mesophilic Prxs. a: Multiple alignments of the protein sequences were performed with CLUSTALW.[36] Red and blue characters indicate -helices and -strands, respectively. The numbers are given as for the sequence of ApTPx. Cys207, which is replaced by Ser in the C207S mutant, is underlined. Sequence homology between ApTPx and PrxII, AhpC, and TryP in the N-terminal segment of the main domain (the region N-terminal to a triangle) is 62, 56, and 54%, respectively. ApTPx, thioredoxin peroxidase from A. pernix; PrxII, peroxiredoxin II from human; AhpC, AhpC from Salmonella typhimurium; TryP, tryparedoxin peroxidase from Crithidia fasciculata. b: Superimposition of the four Prxs aligned in (a). The view of ApTPx structure is the same as in Figure 1(a). Blue, ApTPx; yellow, Prx II; red, TryP; green, AhpC.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 62, 822-826) copyright 2006.