PDBsum entry 2cv4

Oxygen storage/transport

PDB id: 2cv4

Contents

Protein chains

(+ 4 more) 241 a.a. *

Ligands

MES ×2

IPA ×9

Waters ×814

* Residue conservation analysis

PDB id:

2cv4

Name:

Oxygen storage/transport

Title:

Crystal structure of an archaeal peroxiredoxin from the aerobic hyperthermophilic crenarchaeon aeropyrum pernix k1

Structure:

Peroxiredoxin. Chain: a, b, c, d, e, f, g, h, i, j. Engineered: yes

Source:

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

Biol. unit:

Decamer (from PQS)

Resolution:

2.30Å R-factor: 0.178 R-free: 0.230

Authors:

E.Mizohata,H.Sakai,E.Fusatomi,T.Terada,K.Murayama,M.Shirouzu, S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

E.Mizohata et al. (2005). Crystal structure of an archaeal peroxiredoxin from the aerobic hyperthermophilic crenarchaeon Aeropyrum pernix K1. J Mol Biol, 354, 317-329. PubMed id: 16214169 DOI: 10.1016/j.jmb.2005.09.006

Date:

31-May-05 Release date: 14-Jun-05

Supersedes:

1vgs

Protein chains

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

Seq: 250 a.a.

Struc: 241 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: 10.1016/j.jmb.2005.09.006

J Mol Biol 354:317-329 (2005)

PubMed id: 16214169

Crystal structure of an archaeal peroxiredoxin from the aerobic hyperthermophilic crenarchaeon Aeropyrum pernix K1.

E.Mizohata, H.Sakai, E.Fusatomi, T.Terada, K.Murayama, M.Shirouzu, S.Yokoyama.

ABSTRACT

Peroxiredoxins (Prxs) are thiol-dependent peroxidases that catalyze the detoxification of various peroxide substrates such as H2O2, peroxinitrite, and hydroperoxides, and control some signal transduction in eukaryotic cells. Prxs are found in all cellular organisms and represent an enormous superfamily. Recent genome sequencing projects and biochemical studies have identified a novel subfamily, the archaeal Prxs. Their primary sequences are similar to those of the 1-Cys Prxs, which use only one cysteine residue in catalysis, while their catalytic properties resemble those of the typical 2-Cys Prxs, which utilize two cysteine residues from adjacent monomers within a dimer in catalysis. We present here the X-ray crystal structure of an archaeal Prx from the aerobic hyperthermophilic crenarchaeon, Aeropyrum pernix K1, determined at 2.3 A resolution (Rwork of 17.8% and Rfree of 23.0%). The overall subunit arrangement of the A.pernix archaeal Prx is a toroid-shaped pentamer of homodimers, or an (alpha2)5 decamer, as observed in the previously reported crystal structures of decameric Prxs. The basic folding topology and the peroxidatic active site structure are essentially the same as those of the 1-Cys Prx, hORF6, except that the C-terminal extension of the A.pernix archaeal Prx forms a unique helix with its flanking loops. The thiol group of the peroxidatic cysteine C50 is overoxidized to sulfonic acid. Notably, the resolving cysteine C213 forms the intra-monomer disulfide bond with the third cysteine, C207, which should be a unique structural characteristic in the many archaeal Prxs that retain two conserved cysteine residues in the C-terminal region. The conformational flexibility near the intra-monomer disulfide linkage might be necessary for the dramatic structural rearrangements that occur in the catalytic cycle.

Selected figure(s)

Figure 3.
Figure 3. Topology diagram of the A. pernix archaeal Prx. The secondary structure was defined by the program DSSP.53 The a-helices and the b-strands from the N-terminal domain are green and orange, and those from the C-terminal domain are blue and yellow, respectively. The beginnings and the ends of the secondary structural elements are labeled. The positions of the three redox-active cysteine residues (C[P]50, C207 and C[R]213) are shown with red stars.

Figure 8.
Figure 8. Ribbon diagrams of the peroxidatic active sites. The typical 2-Cys Prx adopts (a) fully folded (PDB ID 1QMV)17 and (b) locally unfolded (1QQ2)16 conformations that are correlated with the catalytic cycle. In the recycling step, a dramatic structural rearrangement occurs in order to allow C[P] and C[R] to react and form a disulfide, through the local unfolding of the a2 region and the C-terminal domain. (c) The A. pernix archaeal Prx structure in the fully folded conformation (2CV4, this study). Multiple conformations of the flexible region III (residues 197-206) from ten monomers are drawn in the Figure. The intra-monomer C207-S-S-C[R]213 minimizes the conformational flexibility of region III and suppresses the structural rearrangement leading to the locally unfolded conformation. (d) A model of the locally unfolded conformation for the A. pernix archaeal Prx. The breakage of the intra-monomer C207-S-S-C[R]213 by unknown electron donor(s) would induce the structural rearrangement so that C[R]213-SH can access and react with the C[P]50-SOH, to form the inter-monomer C[P]50-S-S-C[R]213. Helices and b-strands of monomer A are blue and cyan, and those of monomer B are red and pink.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 354, 317-329) copyright 2005.

Figures were selected by an automated process.