PDBsum entry 6e8l

Oxidoreductase

PDB id: 6e8l

Contents

Protein chains

(+ 0 more) 180 a.a.

Waters ×226

PDB id:

6e8l

Name:

Oxidoreductase

Title:

Crystal structure of alkyl hydroperoxidase d (ahpd) from streptococcus pneumoniae (strain d39/ nctc 7466)

Structure:

Alkyl hydroperoxide reductase ahpd. Chain: a, b, c, d, e, f. Engineered: yes

Source:

Streptococcus pneumoniae serotype 2 (strain d39 / nctc 7466). Organism_taxid: 373153. Strain: d39 / nctc 7466. Gene: spd_0373. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.30Å R-factor: 0.196 R-free: 0.242

Authors:

Y.Meng,J.Davies,R.North,D.Coombes,C.Horne,M.Hampton,R.Dobson

Key ref:

Y.Meng et al. (2020). Structure-function analyses of alkylhydroperoxidase D from Streptococcus pneumoniae reveal an unusual three-cysteine active site architecture. J Biol Chem, 295, 2984-2999. PubMed id: 31974167 DOI: 10.1074/jbc.RA119.012226

Date:

30-Jul-18 Release date: 28-Aug-19

Protein chains

A0A0H2ZNM1  (A0A0H2ZNM1_STRP2) -  Carboxymuconolactone decarboxylase-like domain-containing protein from Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)

Seq: 182 a.a.

Struc: 180 a.a.

Enzyme reactions

• Enzyme class: E.C.1.11.1.15 - Transferred entry: 1.11.1.24, 1.11.1.25, 1.11.1.26, 1.11.1.27, 1.11.1.28
• 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

reference

DOI no: 10.1074/jbc.RA119.012226

J Biol Chem 295:2984-2999 (2020)

PubMed id: 31974167

Structure-function analyses of alkylhydroperoxidase D from Streptococcus pneumoniae reveal an unusual three-cysteine active site architecture.

Y.Meng, C.R.Sheen, N.J.Magon, M.B.Hampton, R.C.J.Dobson.

ABSTRACT

During aerobic growth, the Gram-positive facultative anaerobe and opportunistic human pathogen Streptococcus pneumoniae generates large amounts of hydrogen peroxide that can accumulate to millimolar concentrations. The mechanism by which this catalase-negative bacterium can withstand endogenous hydrogen peroxide is incompletely understood. The enzyme alkylhydroperoxidase D (AhpD) has been shown to contribute to pneumococcal virulence and oxidative stress responses in vivo We demonstrate here that SpAhpD exhibits weak thiol-dependent peroxidase activity and, unlike the previously reported Mycobacterium tuberculosis AhpC/D system, SpAhpD does not mediate electron transfer to SpAhpC. A 2.3-Å resolution crystal structure revealed several unusual structural features, including a three-cysteine active site architecture that is buried in a deep pocket, in contrast to the two-cysteine active site found in other AhpD enzymes. All single-cysteine SpAhpD variants remained partially active, and LC-MS/MS analyses revealed that the third cysteine, Cys-163, formed disulfide bonds with either of two cysteines in the canonical Cys-78-X-X-Cys-81 motif. We observed that SpAhpD formed a dimeric quaternary structure both in the crystal and in solution, and that the highly conserved Asn-76 of the AhpD core motif is important for SpAhpD folding. In summary, SpAhpD is a weak peroxidase and does not transfer electrons to AhpC, and therefore does not fit existing models of bacterial AhpD antioxidant defense mechanisms. We propose that it is unlikely that SpAhpD removes peroxides either directly or via AhpC, and that SpAhpD cysteine oxidation may act as a redox switch or mediate electron transfer with other thiol proteins.