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Q5JI79

- AGOG_THEKO

UniProt

Q5JI79 - AGOG_THEKO

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Protein
N-glycosylase/DNA lyase
Gene
TK0940
Organism
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed - Annotation score: 3 out of 5 - Protein inferred from homologyi

Functioni

DNA repair enzyme that is part of the base excision repair (BER) pathway; protects from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine (GO), from single- and double-stranded DNA substrates By similarity.UniRule annotation

Catalytic activityi

The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei43 – 4318-oxoguanine By similarity
Binding sitei71 – 7118-oxoguanine; via carbonyl oxygen By similarity
Binding sitei82 – 8218-oxoguanine By similarity
Active sitei164 – 1641Schiff-base intermediate with DNA By similarity
Binding sitei168 – 16818-oxoguanine By similarity
Binding sitei194 – 19418-oxoguanine; via carbonyl oxygen By similarity
Active sitei196 – 1961 Reviewed prediction
Binding sitei230 – 23018-oxoguanine By similarity
Binding sitei234 – 23418-oxoguanine By similarity

GO - Molecular functioni

  1. DNA-(apurinic or apyrimidinic site) lyase activity Source: UniProtKB-HAMAP
  2. oxidized base lesion DNA N-glycosylase activity Source: UniProtKB-HAMAP
Complete GO annotation...

GO - Biological processi

  1. base-excision repair Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Lyase

Keywords - Biological processi

DNA damage, DNA excision, DNA repair

Enzyme and pathway databases

BioCyciTKOD69014:GH72-953-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
N-glycosylase/DNA lyase
Alternative name(s):
8-oxoguanine DNA glycosylase (EC:3.2.2.-)
AGOG
DNA-(apurinic or apyrimidinic site) lyase (EC:4.2.99.18)
Short name:
AP lyase
Gene namesi
Ordered Locus Names:TK0940
OrganismiThermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Taxonomic identifieri69014 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
ProteomesiUP000000536: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 263263N-glycosylase/DNA lyaseUniRule annotation
PRO_0000185116Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi69014.TK0940.

Structurei

3D structure databases

ProteinModelPortaliQ5JI79.
SMRiQ5JI79. Positions 17-253.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni139 – 20466Helix-hairpin-helixUniRule annotation
Add
BLAST

Domaini

Contains two alpha-helical subdomains, with the 8-oxoguanine binding site located in a cleft at their interface. Contains a helix-hairpin-helix (HhH) structural motif and a Gly/Pro-rich sequence followed by a conserved Asp (HhH-GPD motif).UniRule annotation

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG4047.
HOGENOMiHOG000254352.
KOiK01741.
OMAiVKMFGYA.

Family and domain databases

Gene3Di1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
HAMAPiMF_01168. AGOG.
InterProiIPR011257. DNA_glycosylase.
IPR023170. HTH_base_excis_C.
IPR015254. N-Glyclase/DNA_lyase-like_arc.
IPR016544. N-Glyclase/DNA_lyase_arc.
[Graphical view]
PfamiPF09171. DUF1886. 1 hit.
[Graphical view]
PIRSFiPIRSF008955. AGOG. 1 hit.
SUPFAMiSSF48150. SSF48150. 1 hit.

Sequencei

Sequence statusi: Complete.

Q5JI79-1 [UniParc]FASTAAdd to Basket

« Hide

MSLERFVKIK YQTNEEKADK LVEGLKELGI ECARIIEEKV DLQFDALRHL    50
RENLNDDETF IKLVIANSIV SYQLSGKGED WWWEFSKYFS QNPPEKSIVE 100
ACSKFLPSSR TNRRLVAGKI KRLEKLEPFL NSLTLQELRR YYFENMMGLR 150
NDIAEALGSP KTAKTVVFAV KMFGYAGRIA FGEFVPYPME IDIPEDVRIK 200
AYTERITNEP PVSFWRRVAE ETGIPPLHID SILWPVLGGK REVMERLKKV 250
CEKWELVLEL GSL 263
Length:263
Mass (Da):30,553
Last modified:February 15, 2005 - v1
Checksum:iDBBD7B55740CDBDB
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP006878 Genomic DNA. Translation: BAD85129.1.
RefSeqiYP_183353.1. NC_006624.1.

Genome annotation databases

EnsemblBacteriaiBAD85129; BAD85129; TK0940.
GeneIDi3234448.
KEGGitko:TK0940.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP006878 Genomic DNA. Translation: BAD85129.1 .
RefSeqi YP_183353.1. NC_006624.1.

3D structure databases

ProteinModelPortali Q5JI79.
SMRi Q5JI79. Positions 17-253.
ModBasei Search...

Protein-protein interaction databases

STRINGi 69014.TK0940.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAD85129 ; BAD85129 ; TK0940 .
GeneIDi 3234448.
KEGGi tko:TK0940.

Phylogenomic databases

eggNOGi COG4047.
HOGENOMi HOG000254352.
KOi K01741.
OMAi VKMFGYA.

Enzyme and pathway databases

BioCyci TKOD69014:GH72-953-MONOMER.

Family and domain databases

Gene3Di 1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
HAMAPi MF_01168. AGOG.
InterProi IPR011257. DNA_glycosylase.
IPR023170. HTH_base_excis_C.
IPR015254. N-Glyclase/DNA_lyase-like_arc.
IPR016544. N-Glyclase/DNA_lyase_arc.
[Graphical view ]
Pfami PF09171. DUF1886. 1 hit.
[Graphical view ]
PIRSFi PIRSF008955. AGOG. 1 hit.
SUPFAMi SSF48150. SSF48150. 1 hit.
ProtoNeti Search...

Publicationsi

  1. "Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes."
    Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.
    Genome Res. 15:352-363(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-918 / JCM 12380 / KOD1.

Entry informationi

Entry nameiAGOG_THEKO
AccessioniPrimary (citable) accession number: Q5JI79
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: February 15, 2005
Last modified: May 14, 2014
This is version 56 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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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