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Protein

N-glycosylase/DNA lyase

Gene

PAE2237

Organism
Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827)
Status
Reviewed-Annotation score: Annotation score: 5 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.1 Publication

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.1 Publication

Temperature dependencei

Highly thermostable. No decrease in activity was observed after heating 15 minutes at 80 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei31 – 3118-oxoguanine
Binding sitei58 – 5818-oxoguanine; via carbonyl oxygen
Binding sitei69 – 6918-oxoguanine
Active sitei140 – 1401Schiff-base intermediate with DNA
Binding sitei144 – 14418-oxoguanineSequence Analysis
Binding sitei170 – 17018-oxoguanine; via carbonyl oxygen
Active sitei172 – 1721Sequence Analysis
Binding sitei218 – 21818-oxoguanine
Binding sitei222 – 22218-oxoguanine

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

BioCyciPAER178306:GCEO-1610-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
N-glycosylase/DNA lyase
Alternative name(s):
8-oxoguanine DNA glycosylase (EC:3.2.2.-)
AGOG
DNA-(apurinic or apyrimidinic site) lyase (EC:4.2.99.18)
Short name:
AP lyase
Pa-AGOG
Gene namesi
Ordered Locus Names:PAE2237
OrganismiPyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827)
Taxonomic identifieri178306 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiThermoprotealesThermoproteaceaePyrobaculum
ProteomesiUP000002439: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi140 – 1401K → Q: Loss of activity. 1 Publication
Mutagenesisi147 – 1471K → Q: Great decrease in activity and thermostability. 1 Publication
Mutagenesisi166 – 1661D → N: No effect. 1 Publication
Mutagenesisi172 – 1721D → N: Loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 256256N-glycosylase/DNA lyasePRO_0000185112Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi178306.PAE2237.

Structurei

Secondary structure

1
256
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1412Combined sources
Helixi19 – 268Combined sources
Helixi30 – 4213Combined sources
Helixi44 – 5613Combined sources
Helixi65 – 7713Combined sources
Helixi84 – 9411Combined sources
Helixi102 – 11211Combined sources
Helixi122 – 13312Combined sources
Helixi140 – 15718Combined sources
Helixi173 – 1819Combined sources
Helixi189 – 1946Combined sources
Helixi196 – 21015Combined sources
Helixi214 – 22815Combined sources
Beta strandi235 – 2373Combined sources
Helixi239 – 2446Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XQOX-ray1.03A1-256[»]
1XQPX-ray1.69A1-256[»]
ProteinModelPortaliQ8ZVK6.
SMRiQ8ZVK6. Positions 2-254.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8ZVK6.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni125 – 18460Helix-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).1 Publication

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG4047.
HOGENOMiHOG000222574.
InParanoidiQ8ZVK6.
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.

Q8ZVK6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAAESQLKRV IETLRRLGIE EVLKLERRDP QYRAVCNVVK RHGETVGSRL
60 70 80 90 100
AMLNALISYR LTGKGEEHWE YFGKYFSQLE VIDLCRDFLK YIETSPFLKI
110 120 130 140 150
GVEARKKRAL KACDYVPNLE DLGLTLRQLS HIVGARREQK TLVFTIKILN
160 170 180 190 200
YAYMCSRGVN RVLPFDIPIP VDYRVARLTW CAGLIDFPPE EALRRYEAVQ
210 220 230 240 250
KIWDAVARET GIPPLHLDTL LWLAGRAVLY GENLHGVPKE VIALFQWRGG

CRPPSE
Length:256
Mass (Da):29,467
Last modified:March 1, 2002 - v1
Checksum:iE188433A957C9A16
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009441 Genomic DNA. Translation: AAL64050.1.
RefSeqiNP_559868.1. NC_003364.1.

Genome annotation databases

EnsemblBacteriaiAAL64050; AAL64050; PAE2237.
GeneIDi1464384.
KEGGipai:PAE2237.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009441 Genomic DNA. Translation: AAL64050.1.
RefSeqiNP_559868.1. NC_003364.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XQOX-ray1.03A1-256[»]
1XQPX-ray1.69A1-256[»]
ProteinModelPortaliQ8ZVK6.
SMRiQ8ZVK6. Positions 2-254.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi178306.PAE2237.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL64050; AAL64050; PAE2237.
GeneIDi1464384.
KEGGipai:PAE2237.

Phylogenomic databases

eggNOGiCOG4047.
HOGENOMiHOG000222574.
InParanoidiQ8ZVK6.
KOiK01741.
OMAiVKMFGYA.

Enzyme and pathway databases

BioCyciPAER178306:GCEO-1610-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ8ZVK6.

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. "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.

Entry informationi

Entry nameiAGOG_PYRAE
AccessioniPrimary (citable) accession number: Q8ZVK6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: March 1, 2002
Last modified: March 4, 2015
This is version 66 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.