PDBsum entry 3a2v

Oxidoreductase

PDB id

3a2v

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Contents

			Protein chains

					(+ 4 more) 243 a.a. *

			Ligands

					PER ×10

			Waters ×910

* Residue conservation analysis

PDB id:

3a2v

Links

Name:

Oxidoreductase

Title:

Peroxiredoxin (c207s) from aeropyrum pernix k1 complexed with hydrogen peroxide

Structure:

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

Source:

Aeropyrum pernix. Organism_taxid: 272557. Strain: k1. Gene: ape_2278. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.65Å

R-factor:

0.195

R-free:

0.223

Authors:

T.Nakamura,Y.Kado,F.Yamaguchi,K.Ishikawa,H.Matsumura,T.Inoue

Key ref:

T.Nakamura et al. (2010). Crystal structure of peroxiredoxin from Aeropyrum pernix K1 complexed with its substrate, hydrogen peroxide. J Biochem (tokyo), 147, 109-115. PubMed id: 19819903

Date:

04-Jun-09

Release date:

27-Oct-09

PROCHECK

	Headers

	References

Protein chains

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

Seq: Struc:					250 a.a. 243 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

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



		Enzyme reactions

Enzyme class:

E.C.1.11.1.24 - thioredoxin-dependent peroxiredoxin.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

a hydroperoxide + [thioredoxin]-dithiol = an alcohol + [thioredoxin]- disulfide + H2O

hydroperoxide	+	[thioredoxin]-dithiol Bound ligand (Het Group name = PER) matches with 66.67% similarity	=	alcohol	+	[thioredoxin]- disulfide	+	H2O

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

Added reference

	J Biochem (tokyo) 147:109-115 (2010)
PubMed id: 19819903

Crystal structure of peroxiredoxin from Aeropyrum pernix K1 complexed with its substrate, hydrogen peroxide.
T.Nakamura, Y.Kado, T.Yamaguchi, H.Matsumura, K.Ishikawa, T.Inoue.

ABSTRACT

Peroxiredoxin (Prx) reduces hydrogen peroxide and alkyl peroxides to water and corresponding alcohols, respectively. The reaction is dependent on a peroxidatic cysteine, whose sulphur atom nucleophilically attacks one of the oxygen atoms of the peroxide substrate. In spite of the many structural studies that have been carried out on this reaction, the tertiary structure of the hydrogen peroxide-bound form of Prx has not been elucidated. In this paper, we report the crystal structure of Prx from Aeropyrum pernix K1 in the peroxide-bound form. The conformation of the polypeptide chain is the same as that in the reduced apo-form. The hydrogen peroxide molecule is in close contact with the peroxidatic Cys50 and the neighbouring Thr47 and Arg126 side chain atoms, as well as with the main chain nitrogen atoms of Val49 and Cys50. Bound peroxide was also observed in the mutant C50S, in which the peroxidatic cysteine was replaced by serine. Therefore, the sulphur atom of the peroxidatic cysteine is not essential for peroxide binding, although it enhances the binding affinity. Hydrogen peroxide binds to the protein so that it fills the active site pocket. This study provides insight into the early stage of the Prx reaction.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21182595

T.Nakamura, K.Torikai, K.Uegaki, J.Morita, K.Machida, A.Suzuki, and Y.Kawata (2011).
Crystal structure of the cambialistic superoxide dismutase from Aeropyrum pernix K1--insights into the enzyme mechanism and stability.

FEBS J, 278, 598-609.

PDB codes:

3ak1 3ak2 3ak3

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.