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Protein

N-glycosylase/DNA lyase

Gene

PH1229

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
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 sitei24 – 2418-oxoguanineUniRule annotation
Binding sitei51 – 5118-oxoguanine; via carbonyl oxygenUniRule annotation
Binding sitei62 – 6218-oxoguanineUniRule annotation
Active sitei142 – 1421Schiff-base intermediate with DNAUniRule annotation
Binding sitei146 – 14618-oxoguanineUniRule annotation
Binding sitei172 – 17218-oxoguanine; via carbonyl oxygenUniRule annotation
Active sitei174 – 1741UniRule annotation
Binding sitei208 – 20818-oxoguanineUniRule annotation
Binding sitei212 – 21218-oxoguanineUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Lyase

Keywords - Biological processi

DNA damage, DNA excision, DNA repair

Enzyme and pathway databases

BioCyciPHOR70601:GJWR-1224-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:PH1229
OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Taxonomic identifieri70601 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
ProteomesiUP000000752 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 239239N-glycosylase/DNA lyasePRO_0000185115Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi70601.PH1229.

Structurei

3D structure databases

ProteinModelPortaliO58954.
SMRiO58954. Positions 2-238.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni118 – 18265Helix-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.
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.

O58954-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIAELIREIG IEGARFIEEN IDEQFKALSY LSEGMDRVNF VRLVIANALV
60 70 80 90 100
SYQLTGKGEM WWWEFAKYFK GKEVKTIYSA YKEFLPNSKF NRRLIQQKLL
110 120 130 140 150
RIKKIEPFLS TLTEESIERY YEDMTLLWKA IAKVLKVDRE SKTVVFSVKM
160 170 180 190 200
FGYAARIVLS KFNPYPMEIP IPEDVRIIKL TRKLTNERPR DFWMKIAKES
210 220 230
NVPPLHIDSI LWPLLGGARV EEAPPELKEK LEKLIRVIR
Length:239
Mass (Da):28,191
Last modified:August 1, 1998 - v1
Checksum:i5EC26389EBB5B99E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA30329.1.
PIRiG71066.
RefSeqiNP_143123.1. NC_000961.1.
WP_010885316.1. NC_000961.1.

Genome annotation databases

EnsemblBacteriaiBAA30329; BAA30329; BAA30329.
GeneIDi1443551.
KEGGipho:PH1229.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA30329.1.
PIRiG71066.
RefSeqiNP_143123.1. NC_000961.1.
WP_010885316.1. NC_000961.1.

3D structure databases

ProteinModelPortaliO58954.
SMRiO58954. Positions 2-238.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi70601.PH1229.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA30329; BAA30329; BAA30329.
GeneIDi1443551.
KEGGipho:PH1229.

Phylogenomic databases

eggNOGiCOG4047.
HOGENOMiHOG000254352.
KOiK01741.
OMAiVKMFGYA.

Enzyme and pathway databases

BioCyciPHOR70601:GJWR-1224-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.

Entry informationi

Entry nameiAGOG_PYRHO
AccessioniPrimary (citable) accession number: O58954
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: August 1, 1998
Last modified: April 29, 2015
This is version 76 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

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.