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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: 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.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-oxoguanineUniRule annotation
Binding sitei71 – 7118-oxoguanine; via carbonyl oxygenUniRule annotation
Binding sitei82 – 8218-oxoguanineUniRule annotation
Active sitei164 – 1641Schiff-base intermediate with DNAUniRule annotation
Binding sitei168 – 16818-oxoguanineUniRule annotation
Binding sitei194 – 19418-oxoguanine; via carbonyl oxygenUniRule annotation
Active sitei196 – 1961UniRule annotation
Binding sitei230 – 23018-oxoguanineUniRule annotation
Binding sitei234 – 23418-oxoguanineUniRule annotation

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

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 lyaseUniRule annotation
Alternative name(s):
8-oxoguanine DNA glycosylaseUniRule annotation (EC:3.2.2.-UniRule annotation)
AGOGUniRule annotation
DNA-(apurinic or apyrimidinic site) lyaseUniRule annotation (EC:4.2.99.18UniRule annotation)
Short name:
AP lyaseUniRule annotation
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 lyasePRO_0000185116Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi69014.TK0940.

Structurei

3D structure databases

ProteinModelPortaliQ5JI79.
SMRiQ5JI79. Positions 17-253.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni139 – 20466Helix-hairpin-helixAdd
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).

Sequence similaritiesi

Belongs to the archaeal N-glycosylase/DNA lyase (AGOG) family.UniRule annotation

Phylogenomic databases

eggNOGiCOG4047.
HOGENOMiHOG000254352.
InParanoidiQ5JI79.
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

        10         20         30         40         50
MSLERFVKIK YQTNEEKADK LVEGLKELGI ECARIIEEKV DLQFDALRHL
60 70 80 90 100
RENLNDDETF IKLVIANSIV SYQLSGKGED WWWEFSKYFS QNPPEKSIVE
110 120 130 140 150
ACSKFLPSSR TNRRLVAGKI KRLEKLEPFL NSLTLQELRR YYFENMMGLR
160 170 180 190 200
NDIAEALGSP KTAKTVVFAV KMFGYAGRIA FGEFVPYPME IDIPEDVRIK
210 220 230 240 250
AYTERITNEP PVSFWRRVAE ETGIPPLHID SILWPVLGGK REVMERLKKV
260
CEKWELVLEL GSL
Length:263
Mass (Da):30,553
Last modified:February 15, 2005 - v1
Checksum:iDBBD7B55740CDBDB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
Links Updated
AP006878 Genomic DNA. Translation: BAD85129.1.
RefSeqiYP_183353.1. NC_006624.1.

3D structure databases

ProteinModelPortaliQ5JI79.
SMRiQ5JI79. Positions 17-253.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi69014.TK0940.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiCOG4047.
HOGENOMiHOG000254352.
InParanoidiQ5JI79.
KOiK01741.
OMAiVKMFGYA.

Enzyme and pathway databases

BioCyciTKOD69014:GH72-953-MONOMER.

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.
ProtoNetiSearch...

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: January 7, 2015
This is version 59 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

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 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.