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Q8U2D5 (AGOG_PYRFU) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 62. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
N-glycosylase/DNA lyase
Alternative name(s):
8-oxoguanine DNA glycosylase
EC=3.2.2.-
AGOG
DNA-(apurinic or apyrimidinic site) lyase
Short name=AP lyase
EC=4.2.99.18
Gene names
Ordered Locus Names:PF0904
OrganismPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) [Reference proteome] [HAMAP]
Taxonomic identifier186497 [NCBI]
Taxonomic lineageArchaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus ›

Protein attributes

Sequence length242 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. HAMAP-Rule MF_01168

Catalytic activity

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. HAMAP-Rule MF_01168

Domain

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). HAMAP-Rule MF_01168

Sequence similarities

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 242242N-glycosylase/DNA lyase HAMAP-Rule MF_01168
PRO_0000185114

Regions

Region120 – 18465Helix-hairpin-helix HAMAP-Rule MF_01168

Sites

Active site1441Schiff-base intermediate with DNA By similarity
Active site1761 Potential
Binding site2618-oxoguanine By similarity
Binding site5318-oxoguanine; via carbonyl oxygen By similarity
Binding site6418-oxoguanine By similarity
Binding site14818-oxoguanine By similarity
Binding site17418-oxoguanine; via carbonyl oxygen By similarity
Binding site21018-oxoguanine By similarity
Binding site21418-oxoguanine By similarity

Secondary structure

1 ............................ 242
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q8U2D5 [UniParc].

Last modified June 1, 2002. Version 1.
Checksum: 6FA190D348D3E823

FASTA24228,345
        10         20         30         40         50         60 
MRELVEIIKG IGIEGAKEVE EKVDRQFYAL QYLFRHQDPE MFIKLVIANS LVSYQLTGRG 

        70         80         90        100        110        120 
EDWWWEFARY FSGREVDSIW KAYGEFLPKS KNNRRLIEAK LNRIRKVEGF LSTLTLKDLE 

       130        140        150        160        170        180 
GYYKNMKMLW KALIKIMGSR EDSKTIVFTV KMFGYASRIA FSRFIPYPME IPIPEDLRIK 

       190        200        210        220        230        240 
SVTSKLTQEK PTKFWMKIGQ ESGVPPLHID SLIWPLLGNA DLTPLDIELR NKLMKLTELL 


GL

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AE009950 Genomic DNA. Translation: AAL81028.1.
RefSeqNP_578633.2. NC_003413.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1XG7X-ray1.88A/B2-242[»]
ProteinModelPortalQ8U2D5.
SMRQ8U2D5. Positions 2-242.
ModBaseSearch...

Protein-protein interaction databases

STRING186497.PF0904.

Proteomic databases

PRIDEQ8U2D5.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAL81028; AAL81028; PF0904.
GeneID1468768.
KEGGpfu:PF0904.

Phylogenomic databases

eggNOGCOG4047.
HOGENOMHOG000254352.
KOK01741.
OMAVKMFGYA.
ProtClustDBPRK13280.

Family and domain databases

Gene3D1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
HAMAPMF_01168. AGOG.
InterProIPR011257. DNA_glycosylase.
IPR023170. HTH_base_excis_C.
IPR015254. N-Glyclase/DNA_lyase-like_arc.
IPR016544. N-Glyclase/DNA_lyase_arc.
[Graphical view]
PfamPF09171. DUF1886. 1 hit.
[Graphical view]
PIRSFPIRSF008955. AGOG. 1 hit.
SUPFAMSSF48150. DNA_glycsylse. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ8U2D5.

Entry information

Entry nameAGOG_PYRFU
AccessionPrimary (citable) accession number: Q8U2D5
Entry history
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: June 1, 2002
Last modified: May 1, 2013
This is version 62 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents