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Protein

Alkyl hydroperoxide reductase AhpD

Gene

ahpD

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity.
Together with AhpC, DlaT and Lpd, constitutes an NADH-dependent peroxidase active against hydrogen and alkyl peroxides as well as serving as a peroxynitrite reductase, thus protecting the bacterium against reactive nitrogen intermediates and oxidative stress generated by the host immune system.

Catalytic activityi

2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.UniRule annotation

pH dependencei

Optimum pH is 7.2.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei130 – 1301Proton donorUniRule annotation1 Publication
Active sitei133 – 1331Cysteine sulfenic acid (-SOH) intermediateUniRule annotation1 Publication

GO - Molecular functioni

  • alkyl hydroperoxide reductase activity Source: UniProtKB-HAMAP
  • disulfide oxidoreductase activity Source: MTBBASE
  • hydroperoxide reductase activity Source: MTBBASE
  • peroxidase activity Source: UniProtKB-KW
  • peroxiredoxin activity Source: UniProtKB-EC

GO - Biological processi

  • cell redox homeostasis Source: MTBBASE
  • response to oxidative stress Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Antioxidant, Oxidoreductase, Peroxidase

Enzyme and pathway databases

ReactomeiR-HSA-1222541. Cell redox homeostasis.

Names & Taxonomyi

Protein namesi
Recommended name:
Alkyl hydroperoxide reductase AhpDUniRule annotation (EC:1.11.1.15UniRule annotation)
Alternative name(s):
Alkylhydroperoxidase AhpDUniRule annotation
Gene namesi
Name:ahpDUniRule annotation
Ordered Locus Names:Rv2429
ORF Names:MTCY428.17c
OrganismiMycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Taxonomic identifieri83332 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
Proteomesi
  • UP000001584 Componenti: Chromosome

Organism-specific databases

TubercuListiRv2429.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: Reactome
  • plasma membrane Source: MTBBASE
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi118 – 1181E → Q: Reduces protein stability. No effect on catalytic activity. 1 Publication
Mutagenesisi130 – 1301C → S: Loss of activity. 3 Publications
Mutagenesisi132 – 1321H → F: Slightly reduced catalytic activity. 1 Publication
Mutagenesisi132 – 1321H → Q: Slightly reduced catalytic activity. 1 Publication
Mutagenesisi133 – 1331C → S: Loss of activity. Loss of interchain disulfide bond with AhpC. 3 Publications
Mutagenesisi137 – 1371H → F: Reduced catalytic activity. 1 Publication
Mutagenesisi137 – 1371H → Q: Slightly reduced catalytic activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 177177Alkyl hydroperoxide reductase AhpDPRO_0000064507Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi130 ↔ 1331 Publication
Disulfide bondi133 – 133Interchain (with C-61 in AhpC); in linked form1 Publication

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiP9WQB5.

Interactioni

Subunit structurei

Homotrimer. Identified in a complex with AhpC, DlaT and Lpd.UniRule annotation4 Publications

Protein-protein interaction databases

STRINGi83332.Rv2429.

Structurei

Secondary structure

1
177
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 97Combined sources
Helixi12 – 143Combined sources
Helixi15 – 2410Combined sources
Beta strandi28 – 303Combined sources
Helixi32 – 4514Combined sources
Helixi49 – 5911Combined sources
Turni60 – 623Combined sources
Helixi65 – 9026Combined sources
Turni91 – 977Combined sources
Helixi105 – 1084Combined sources
Helixi114 – 12815Combined sources
Helixi131 – 14313Combined sources
Helixi148 – 17326Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GU9X-ray1.90A/B/C/D/E/F/G/H/I/J/K/L1-177[»]
1KNCX-ray2.00A/B/C1-177[»]
1LW1X-ray2.30A/B/C1-177[»]
1ME5X-ray2.40A/B/C1-177[»]
ProteinModelPortaliP9WQB5.
SMRiP9WQB5. Positions 3-175.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the AhpD family.UniRule annotation

Keywords - Domaini

Redox-active center

Phylogenomic databases

eggNOGiCOG2128. LUCA.
KOiK04756.
OMAiAIMAMNN.
PhylomeDBiP9WQB5.

Family and domain databases

Gene3Di1.20.1290.10. 1 hit.
HAMAPiMF_01676. AhpD.
InterProiIPR004674. AhpD.
IPR029032. AhpD-like.
IPR004675. AhpD_core.
IPR003779. CMD-like.
[Graphical view]
PfamiPF02627. CMD. 1 hit.
[Graphical view]
SUPFAMiSSF69118. SSF69118. 1 hit.
TIGRFAMsiTIGR00777. ahpD. 1 hit.
TIGR00778. ahpD_dom. 1 hit.

Sequencei

Sequence statusi: Complete.

P9WQB5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSIEKLKAAL PEYAKDIKLN LSSITRSSVL DQEQLWGTLL ASAAATRNPQ
60 70 80 90 100
VLADIGAEAT DHLSAAARHA ALGAAAIMGM NNVFYRGRGF LEGRYDDLRP
110 120 130 140 150
GLRMNIIANP GIPKANFELW SFAVSAINGC SHCLVAHEHT LRTVGVDREA
160 170
IFEALKAAAI VSGVAQALAT IEALSPS
Length:177
Mass (Da):18,781
Last modified:April 16, 2014 - v1
Checksum:iB7DD28AA9BD9B24C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U44840 Genomic DNA. Translation: AAA86657.1.
AL123456 Genomic DNA. Translation: CCP45221.1.
PIRiC70679.
RefSeqiNP_216945.1. NC_000962.3.
WP_003412536.1. NZ_KK339370.1.

Genome annotation databases

EnsemblBacteriaiCCP45221; CCP45221; Rv2429.
GeneIDi885959.
KEGGimtu:Rv2429.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U44840 Genomic DNA. Translation: AAA86657.1.
AL123456 Genomic DNA. Translation: CCP45221.1.
PIRiC70679.
RefSeqiNP_216945.1. NC_000962.3.
WP_003412536.1. NZ_KK339370.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GU9X-ray1.90A/B/C/D/E/F/G/H/I/J/K/L1-177[»]
1KNCX-ray2.00A/B/C1-177[»]
1LW1X-ray2.30A/B/C1-177[»]
1ME5X-ray2.40A/B/C1-177[»]
ProteinModelPortaliP9WQB5.
SMRiP9WQB5. Positions 3-175.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi83332.Rv2429.

Proteomic databases

PaxDbiP9WQB5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCCP45221; CCP45221; Rv2429.
GeneIDi885959.
KEGGimtu:Rv2429.

Organism-specific databases

TubercuListiRv2429.

Phylogenomic databases

eggNOGiCOG2128. LUCA.
KOiK04756.
OMAiAIMAMNN.
PhylomeDBiP9WQB5.

Enzyme and pathway databases

ReactomeiR-HSA-1222541. Cell redox homeostasis.

Family and domain databases

Gene3Di1.20.1290.10. 1 hit.
HAMAPiMF_01676. AhpD.
InterProiIPR004674. AhpD.
IPR029032. AhpD-like.
IPR004675. AhpD_core.
IPR003779. CMD-like.
[Graphical view]
PfamiPF02627. CMD. 1 hit.
[Graphical view]
SUPFAMiSSF69118. SSF69118. 1 hit.
TIGRFAMsiTIGR00777. ahpD. 1 hit.
TIGR00778. ahpD_dom. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Zhang Y., Dhandayuthapani S., Deretic V.
    Submitted (JAN-1996) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 25618 / H37Rv.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 25618 / H37Rv.
  3. "The AhpC and AhpD antioxidant defense system of Mycobacterium tuberculosis."
    Hillas P.J., del Alba F.S., Oyarzabal J., Wilks A., Ortiz De Montellano P.R.
    J. Biol. Chem. 275:18801-18809(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT, MUTAGENESIS OF CYS-130 AND CYS-133.
  4. "Intermolecular interactions in the AhpC/AhpD antioxidant defense system of Mycobacterium tuberculosis."
    Koshkin A., Knudsen G.M., Ortiz De Montellano P.R.
    Arch. Biochem. Biophys. 427:41-47(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT, DISULFIDE BONDS.
  5. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ATCC 25618 / H37Rv.
  6. "The crystal structure of Mycobacterium tuberculosis alkylhydroperoxidase AhpD, a potential target for antitubercular drug design."
    Nunn C.M., Djordjevic S., Hillas P.J., Nishida C.R., Ortiz de Montellano P.R.
    J. Biol. Chem. 277:20033-20040(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), ACTIVE SITE, SUBUNIT.
  7. "Metabolic enzymes of mycobacteria linked to antioxidant defense by a thioredoxin-like protein."
    Bryk R., Lima C.D., Erdjument-Bromage H., Tempst P., Nathan C.
    Science 295:1073-1077(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), FUNCTION, SUBUNIT, MUTAGENESIS OF CYS-130 AND CYS-133.
    Strain: ATCC 25618 / H37Rv.
  8. "The mechanism of Mycobacterium tuberculosis alkylhydroperoxidase AhpD as defined by mutagenesis, crystallography, and kinetics."
    Koshkin A., Nunn C.M., Djordjevic S., Ortiz de Montellano P.R.
    J. Biol. Chem. 278:29502-29508(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF MUTANTS GLN-132 AND PHE-137, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF GLU-118; CYS-130; HIS-132; CYS-133 AND HIS-137.

Entry informationi

Entry nameiAHPD_MYCTU
AccessioniPrimary (citable) accession number: P9WQB5
Secondary accession number(s): L0T9S9, P0A5N4, Q57353
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 16, 2014
Last sequence update: April 16, 2014
Last modified: June 8, 2016
This is version 18 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh
    Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.