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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)DescriptionActionsGraphical viewLength
Binding sitei318-oxoguanine1
Binding sitei588-oxoguanine; via carbonyl oxygen1
Binding sitei698-oxoguanine1
Active sitei140Schiff-base intermediate with DNA1
Binding sitei1448-oxoguanineSequence analysis1
Binding sitei1708-oxoguanine; via carbonyl oxygen1
Active sitei172Sequence analysis1
Binding sitei2188-oxoguanine1
Binding sitei2228-oxoguanine1

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

BRENDAi3.2.2.B5. 5239.
4.2.99.18. 5239.

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
Proteomesi
  • UP000002439 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi140K → Q: Loss of activity. 1 Publication1
Mutagenesisi147K → Q: Great decrease in activity and thermostability. 1 Publication1
Mutagenesisi166D → N: No effect. 1 Publication1
Mutagenesisi172D → N: Loss of activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001851121 – 256N-glycosylase/DNA lyaseAdd BLAST256

Interactioni

Protein-protein interaction databases

STRINGi178306.PAE2237.

Structurei

Secondary structure

1256
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 14Combined sources12
Helixi19 – 26Combined sources8
Helixi30 – 42Combined sources13
Helixi44 – 56Combined sources13
Helixi65 – 77Combined sources13
Helixi84 – 94Combined sources11
Helixi102 – 112Combined sources11
Helixi122 – 133Combined sources12
Helixi140 – 157Combined sources18
Helixi173 – 181Combined sources9
Helixi189 – 194Combined sources6
Helixi196 – 210Combined sources15
Helixi214 – 228Combined sources15
Beta strandi235 – 237Combined sources3
Helixi239 – 244Combined sources6

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ8ZVK6.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni125 – 184Helix-hairpin-helixAdd BLAST60

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

eggNOGiarCOG04144. Archaea.
COG4047. LUCA.
HOGENOMiHOG000222574.
InParanoidiQ8ZVK6.
KOiK01741.
OMAiVKMFGYA.

Family and domain databases

Gene3Di1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
HAMAPiMF_01168. AGOG. 1 hit.
InterProiIPR016544. AGOG.
IPR015254. AGOG-like.
IPR011257. DNA_glycosylase.
IPR023170. HTH_base_excis_C.
[Graphical view]
PfamiPF09171. AGOG. 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.

Genome annotation databases

EnsemblBacteriaiAAL64050; AAL64050; PAE2237.
KEGGipai:PAE2237.

Cross-referencesi

Sequence databases

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

3D structure databases

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

Protein-protein interaction databases

STRINGi178306.PAE2237.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL64050; AAL64050; PAE2237.
KEGGipai:PAE2237.

Phylogenomic databases

eggNOGiarCOG04144. Archaea.
COG4047. LUCA.
HOGENOMiHOG000222574.
InParanoidiQ8ZVK6.
KOiK01741.
OMAiVKMFGYA.

Enzyme and pathway databases

BRENDAi3.2.2.B5. 5239.
4.2.99.18. 5239.

Miscellaneous databases

EvolutionaryTraceiQ8ZVK6.

Family and domain databases

Gene3Di1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
HAMAPiMF_01168. AGOG. 1 hit.
InterProiIPR016544. AGOG.
IPR015254. AGOG-like.
IPR011257. DNA_glycosylase.
IPR023170. HTH_base_excis_C.
[Graphical view]
PfamiPF09171. AGOG. 1 hit.
[Graphical view]
PIRSFiPIRSF008955. AGOG. 1 hit.
SUPFAMiSSF48150. SSF48150. 1 hit.
ProtoNetiSearch...

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: November 2, 2016
This is version 75 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

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 one 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.