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Q8ZVK6 (AGOG_PYRAE) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 60. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

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
Pa-AGOG
Gene names
Ordered Locus Names:PAE2237
OrganismPyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827) [Reference proteome] [HAMAP]
Taxonomic identifier178306 [NCBI]
Taxonomic lineageArchaeaCrenarchaeotaThermoproteiThermoprotealesThermoproteaceaePyrobaculum

Protein attributes

Sequence length256 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. Ref.2

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. Ref.2

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). Ref.3

Sequence similarities

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

Biophysicochemical properties

Temperature dependence:

Highly thermostable. No decrease in activity was observed after heating 15 minutes at 80 degrees Celsius. Ref.2

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 256256N-glycosylase/DNA lyase HAMAP-Rule MF_01168
PRO_0000185112

Regions

Region125 – 18460Helix-hairpin-helix HAMAP-Rule MF_01168

Sites

Active site1401Schiff-base intermediate with DNA
Active site1721 Potential
Binding site3118-oxoguanine
Binding site5818-oxoguanine; via carbonyl oxygen
Binding site6918-oxoguanine
Binding site14418-oxoguanine Potential
Binding site17018-oxoguanine; via carbonyl oxygen
Binding site21818-oxoguanine
Binding site22218-oxoguanine

Experimental info

Mutagenesis1401K → Q: Loss of activity. Ref.2
Mutagenesis1471K → Q: Great decrease in activity and thermostability. Ref.2
Mutagenesis1661D → N: No effect. Ref.2
Mutagenesis1721D → N: Loss of activity. Ref.2

Secondary structure

............................... 256
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q8ZVK6 [UniParc].

Last modified March 1, 2002. Version 1.
Checksum: E188433A957C9A16

FASTA25629,467
        10         20         30         40         50         60 
MAAESQLKRV IETLRRLGIE EVLKLERRDP QYRAVCNVVK RHGETVGSRL AMLNALISYR 

        70         80         90        100        110        120 
LTGKGEEHWE YFGKYFSQLE VIDLCRDFLK YIETSPFLKI GVEARKKRAL KACDYVPNLE 

       130        140        150        160        170        180 
DLGLTLRQLS HIVGARREQK TLVFTIKILN YAYMCSRGVN RVLPFDIPIP VDYRVARLTW 

       190        200        210        220        230        240 
CAGLIDFPPE EALRRYEAVQ KIWDAVARET GIPPLHLDTL LWLAGRAVLY GENLHGVPKE 

       250 
VIALFQWRGG CRPPSE 

« Hide

References

« Hide 'large scale' references
[1]"Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum."
Fitz-Gibbon S.T., Ladner H., Kim U.-J., Stetter K.O., Simon M.I., Miller J.H.
Proc. Natl. Acad. Sci. U.S.A. 99:984-989(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827.
[2]"Pa-AGOG, the founding member of a new family of archaeal 8-oxoguanine DNA-glycosylases."
Sartori A.A., Lingaraju G.M., Hunziker P., Winkler F.K., Jiricny J.
Nucleic Acids Res. 32:6531-6539(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF LYS-140; LYS-147; ASP-166 AND ASP-172.
[3]"A DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure."
Lingaraju G.M., Sartori A.A., Kostrewa D., Prota A.E., Jiricny J., Winkler F.K.
Structure 13:87-98(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.0 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH 8-OXOGUANOSINE, DOMAIN.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE009441 Genomic DNA. Translation: AAL64050.1.
RefSeqNP_559868.1. NC_003364.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1XQOX-ray1.03A1-256[»]
1XQPX-ray1.69A1-256[»]
ProteinModelPortalQ8ZVK6.
SMRQ8ZVK6. Positions 2-254.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING178306.PAE2237.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAL64050; AAL64050; PAE2237.
GeneID1464384.
KEGGpai:PAE2237.

Phylogenomic databases

eggNOGCOG4047.
HOGENOMHOG000222574.
KOK01741.
OMAVKMFGYA.

Enzyme and pathway databases

BioCycPAER178306:GCEO-1610-MONOMER.

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. SSF48150. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ8ZVK6.

Entry information

Entry nameAGOG_PYRAE
AccessionPrimary (citable) accession number: Q8ZVK6
Entry history
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: March 1, 2002
Last modified: May 14, 2014
This is version 60 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references