PDBsum entry: 1me5

Oxidoreductase

PDB id: 1me5

Contents

Protein chains

173 a.a. *

Waters ×370

* Residue conservation analysis

PDB id:

1me5

Name:

Oxidoreductase

Title:

Crystal structure of mycobacterium tuberculosis alkylperoxidase ahpd h132q mutant

Structure:

Alkylhydroperoxidase d. Chain: a, b, c. Synonym: ahpd protein. Engineered: yes. Mutation: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PQS)

Resolution:

2.40Å R-factor: 0.223 R-free: 0.350

Authors:

C.M.Nunn,S.Djordjevic,P.R.Ortiz De Montellano

Key ref:

A.Koshkin et al. (2003). The mechanism of Mycobacterium tuberculosis alkylhydroperoxidase AhpD as defined by mutagenesis, crystallography, and kinetics. J Biol Chem, 278, 29502-29508. PubMed id: 12761216 DOI: 10.1074/jbc.M303747200

Date:

08-Aug-02 Release date: 11-Sep-02

Protein chains

P0A5N4  (AHPD_MYCTU) -  Alkyl hydroperoxide reductase AhpD

Seq: 177 a.a.

Struc: 173 a.a.*

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

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 

• Cellular component: plasma membrane (1 term)
• Biological process: oxidation reduction (3 terms)
• Biochemical function: antioxidant activity (7 terms)

reference

DOI no: 10.1074/jbc.M303747200

J Biol Chem 278:29502-29508 (2003)

PubMed id: 12761216

The mechanism of Mycobacterium tuberculosis alkylhydroperoxidase AhpD as defined by mutagenesis, crystallography, and kinetics.

A.Koshkin, C.M.Nunn, S.Djordjevic, P.R.Ortiz de Montellano.

ABSTRACT

AhpD, a protein with two cysteine residues, is required for physiological reduction of the Mycobacterium tuberculosis alkylhydroperoxidase AhpC. AhpD also has an alkylhydroperoxidase activity of its own. The AhpC/AhpD system provides critical antioxidant protection, particularly in the absence of the catalase-peroxidase KatG, which is suppressed in most isoniazid-resistant strains. Based on the crystal structure, we proposed recently a catalytic mechanism for AhpD involving a proton relay in which the Glu118 carboxylate group, via His137 and a water molecule, deprotonates the catalytic residue Cys133 (Nunn, C. M., Djordjevic, S., Hillas, P. J., Nishida, C., and Ortiz de Montellano, P. R. (2002) J. Biol. Chem. 277, 20033-20040). A possible role for His132 in subsequent formation of the Cys133-Cys130 disulfide bond was also noted. To test this proposed mechanism, we have expressed the H137F, H137Q, H132F, H132Q, E118F, E118Q, C133S, and C130S mutants of AhpD, determined the crystal structures of the H137F and H132Q mutants, estimated the pKa values of the cysteine residues, and defined the kinetic properties of the mutant proteins. The collective results strongly support the proposed catalytic mechanism for AhpD.

Selected figure(s)

Figure 7.
FIG. 7. Active site residues for the H132Q mutant (gray; a) and the H137F mutant (gray; b) structures superimposed with those in the native AhpD structure (black) (26).

Figure 8.
FIG. 8. Overlay of AhpD structure with thioredoxin (solid gray). Cys133 and Cys39 (thioredoxin) are overlaid to illustrate the similar separation in the two structures between this Cys and His137 (AhpD) and Asp30 (thioredoxin).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 29502-29508) copyright 2003.

Figures were selected by an automated process.