PDBsum entry 1nm3

Electron transport

PDB id: 1nm3

Contents

Protein chains

237 a.a. *

Ligands

SO4 ×4

* Residue conservation analysis

PDB id:

1nm3

Name:

Electron transport

Title:

Crystal structure of heamophilus influenza hybrid-prx5

Structure:

Protein hi0572. Chain: a, b. Synonym: hybrid peroxiredoxin. Engineered: yes

Source:

Haemophilus influenzae. Organism_taxid: 727. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.80Å R-factor: 0.239 R-free: 0.283

Authors:

S.J.Kim,J.R.Woo,Y.S.Hwang,D.G.Jeong,D.H.Shin,K.H.Kim,S.E.Ryu

Key ref:

S.J.Kim et al. (2003). The tetrameric structure of Haemophilus influenza hybrid Prx5 reveals interactions between electron donor and acceptor proteins. J Biol Chem, 278, 10790-10798. PubMed id: 12529327 DOI: 10.1074/jbc.M209553200

Date:

08-Jan-03 Release date: 25-Mar-03

Protein chains

P44758  (PRX5_HAEIN) -  Hybrid peroxiredoxin hyPrx5 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

Seq: 241 a.a.

Struc: 237 a.a.

Enzyme reactions

• Enzyme class: E.C.1.11.1.27 - glutathione-dependent peroxiredoxin.
• Reaction: a hydroperoxide + 2 glutathione = an alcohol + glutathione disulfide + H2O

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

reference

DOI no: 10.1074/jbc.M209553200

J Biol Chem 278:10790-10798 (2003)

PubMed id: 12529327

The tetrameric structure of Haemophilus influenza hybrid Prx5 reveals interactions between electron donor and acceptor proteins.

S.J.Kim, J.R.Woo, Y.S.Hwang, D.G.Jeong, D.H.Shin, K.Kim, S.E.Ryu.

ABSTRACT

Cellular redox control is often mediated by oxidation and reduction of cysteine residues in the redox-sensitive proteins, where thioredoxin and glutaredoxin (Grx) play as electron donors for the oxidized proteins. Despite the importance of protein-protein interactions between the electron donor and acceptor proteins, there has been no structural information for the interaction of thioredoxin or Grx with natural target proteins. Here, we present the crystal structure of a novel Haemophilus influenza peroxiredoxin (Prx) hybrid Prx5 determined at 2.8-A resolution. The structure reveals that hybrid Prx5 forms a tightly associated tetramer where active sites of Prx and Grx domains of different monomers interact with each other. The Prx-Grx interface comprises specific charge interactions surrounded by weak interactions, providing insight into the target recognition mechanism of Grx. The tetrameric structure also exhibits a flexible active site and alternative Prx-Grx interactions, which appear to facilitate the electron transfer from Grx to Prx domain. Differences of electron donor binding surfaces in Prx proteins revealed by an analysis based on the structural information explain the electron donor specificities of various Prx proteins.

Selected figure(s)

Figure 4.
Fig. 4. Environment of the redox active site. a, Prx-Grx interaction and glutathione binding in the hyPrx5 tetramer. Glutathione model (shown in the figure as a ball and stick diagram) was created by superposing the complex structure of Grx3-glutathione (PDB code 3GRX) on the hyPrx5 Grx domain. Surfaces of Prx (monomer A) and Grx (monomer D) domains are colored red and gold, respectively. Redox active cysteines (Cys-49 and Cys-180) and residues involved in the Prx-Grx interaction are labeled. b, stereo view of the 2F[o] F[c] electron density map. The electron density map around the Prx active site of hyPrx5 is presented as superimposed with the refined model. The map was contoured at a 0.9 level. c, stereo view of the Prx active site of hyPrx5. The side chains of residues (Arg-126 and Thr-46) contributing to the reactivity of the sulfur atom of Cys-49 were drawn as a ball-and-stick representation. Distances between the interacting atoms are shown in the figure.

Figure 5.
Fig. 5. Interaction surfaces implicated in the Prx-Grx or Prx-Trx interaction. Electrostatic potential surfaces of the hyPrx5 Prx domain, the hyPrx5 Grx domain, human Prx5 (PDB code 1HD2), and human Trx (PDB code 1ERU) were calculated by using the program GRASP (27). Positive and negative charges are represented as blue and red, respectively. a, the surface of the hyPrx5 Prx domain. Residues involved in the Prx-Grx contact in the hyPrx5 tetramer are labeled and surrounded by a yellow lines. The alternative interaction surface (see "Prx-Grx Interaction") is indicated with a green line. b, the surface of the hyPrx5 Grx domain. Residues involved in the Prx-Grx contact of in the hyPrx5 tetramer are labeled and surrounded by a yellow line. c, the surface of human Prx5. Residues of human Prx5 corresponding to those participating in the Prx-Grx contact of hyPrx5 are labeled and surrounded by a yellow line. The point of view in the figure is the same as in a. The orientation was determined by superposing the two structures (the hyPrx5 Prx domain and human Prx5). Thr-48, Ser-51, Phe-150, Asp-154, and Asp-156 of the hyPrx5 Prx domain correspond to Gly-46, Lys-49, Leu-149, Leu-153, and Pro-155 of human Prx5, respectively (for the sequence alignment, see Fig. 2). d, the surface of human Trx. Residues of human Trx involved in the Trx-Trx reductase contact (PDB code 1F6M) are labeled and surrounded by a yellow line. The point of view in the figure is the same as in b. The orientation was determined by superposing the two structures (the hyPrx5 Grx domain and human Trx). The C trace of the NF B peptide bound to human Trx (Ref. 38, PDB code 1MDI) was drawn as a cyan tube.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 10790-10798) copyright 2003.

Figures were selected by an automated process.