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Protein

N-glycosylase/DNA lyase

Gene

PF0904

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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 sitei26 – 2618-oxoguanineUniRule annotation
Binding sitei53 – 5318-oxoguanine; via carbonyl oxygenUniRule annotation
Binding sitei64 – 6418-oxoguanineUniRule annotation
Active sitei144 – 1441Schiff-base intermediate with DNAUniRule annotation
Binding sitei148 – 14818-oxoguanineUniRule annotation
Binding sitei174 – 17418-oxoguanine; via carbonyl oxygenUniRule annotation
Active sitei176 – 1761UniRule annotation
Binding sitei210 – 21018-oxoguanineUniRule annotation
Binding sitei214 – 21418-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

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:PF0904
OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Taxonomic identifieri186497 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
ProteomesiUP000001013: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 242242N-glycosylase/DNA lyasePRO_0000185114Add
BLAST

Proteomic databases

PRIDEiQ8U2D5.

Interactioni

Protein-protein interaction databases

STRINGi186497.PF0904.

Structurei

Secondary structure

1
242
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi2 – 2221Combined sources
Helixi25 – 3410Combined sources
Helixi39 – 5113Combined sources
Helixi60 – 7112Combined sources
Helixi79 – 868Combined sources
Turni87 – 893Combined sources
Helixi97 – 11216Combined sources
Helixi116 – 1249Combined sources
Helixi126 – 13712Combined sources
Helixi144 – 16017Combined sources
Helixi177 – 1848Combined sources
Helixi191 – 20212Combined sources
Helixi206 – 21712Combined sources
Helixi227 – 23913Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XG7X-ray1.88A/B2-242[»]
4PIIX-ray2.17A2-242[»]
ProteinModelPortaliQ8U2D5.
SMRiQ8U2D5. Positions 2-242.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8U2D5.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni120 – 18465Helix-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.

Q8U2D5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRELVEIIKG IGIEGAKEVE EKVDRQFYAL QYLFRHQDPE MFIKLVIANS
60 70 80 90 100
LVSYQLTGRG EDWWWEFARY FSGREVDSIW KAYGEFLPKS KNNRRLIEAK
110 120 130 140 150
LNRIRKVEGF LSTLTLKDLE GYYKNMKMLW KALIKIMGSR EDSKTIVFTV
160 170 180 190 200
KMFGYASRIA FSRFIPYPME IPIPEDLRIK SVTSKLTQEK PTKFWMKIGQ
210 220 230 240
ESGVPPLHID SLIWPLLGNA DLTPLDIELR NKLMKLTELL GL
Length:242
Mass (Da):28,345
Last modified:June 1, 2002 - v1
Checksum:i6FA190D348D3E823
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL81028.1.
RefSeqiNP_578633.2. NC_003413.1.

Genome annotation databases

EnsemblBacteriaiAAL81028; AAL81028; PF0904.
GeneIDi1468768.
KEGGipfu:PF0904.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL81028.1.
RefSeqiNP_578633.2. NC_003413.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XG7X-ray1.88A/B2-242[»]
4PIIX-ray2.17A2-242[»]
ProteinModelPortaliQ8U2D5.
SMRiQ8U2D5. Positions 2-242.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi186497.PF0904.

Proteomic databases

PRIDEiQ8U2D5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL81028; AAL81028; PF0904.
GeneIDi1468768.
KEGGipfu:PF0904.

Phylogenomic databases

eggNOGiCOG4047.
HOGENOMiHOG000254352.
KOiK01741.
OMAiVKMFGYA.

Miscellaneous databases

EvolutionaryTraceiQ8U2D5.

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

« Hide 'large scale' publications
  1. "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences."
    Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T.
    Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
  2. "Conserved hypothetical protein Pfu-877259-001 from Pyrococcus furiosus."
    Chang J., Zhao M., Horanyi P., Xu H., Yang H., Liu Z.-J., Chen L., Zhou W., Habel J., Tempel W., Lee D., Lin D., Chang S.-H., Eneh J.C., Hopkins R.C., Jenney F.E., Lee H.-S., Li T.
    , Poole F.L., Shah C., Sugar F.J., Chen C.-Y., Arendall W.B., Richardson J.S., Richardson D.C., Rose J.P.
    Submitted (SEP-2004) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).

Entry informationi

Entry nameiAGOG_PYRFU
AccessioniPrimary (citable) accession number: Q8U2D5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: June 1, 2002
Last modified: March 4, 2015
This is version 69 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.