AGOG_PYRFU
ID AGOG_PYRFU Reviewed; 242 AA.
AC Q8U2D5;
DT 10-JAN-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=N-glycosylase/DNA lyase {ECO:0000255|HAMAP-Rule:MF_01168};
DE AltName: Full=8-oxoguanine DNA glycosylase {ECO:0000255|HAMAP-Rule:MF_01168};
DE EC=3.2.2.- {ECO:0000255|HAMAP-Rule:MF_01168};
DE AltName: Full=AGOG {ECO:0000255|HAMAP-Rule:MF_01168};
DE AltName: Full=DNA-(apurinic or apyrimidinic site) lyase {ECO:0000255|HAMAP-Rule:MF_01168};
DE Short=AP lyase {ECO:0000255|HAMAP-Rule:MF_01168};
DE EC=4.2.99.18 {ECO:0000255|HAMAP-Rule:MF_01168};
GN OrderedLocusNames=PF0904;
OS Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=186497;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=10430560; DOI=10.1093/genetics/152.4.1299;
RA Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M.,
RA DiRuggiero J., Robb F.T.;
RT "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P.
RT horikoshii inferred from complete genomic sequences.";
RL Genetics 152:1299-1305(1999).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
RA Chang J., Zhao M., Horanyi P., Xu H., Yang H., Liu Z.-J., Chen L., Zhou W.,
RA Habel J., Tempel W., Lee D., Lin D., Chang S.-H., Eneh J.C., Hopkins R.C.,
RA Jenney F.E., Lee H.-S., Li T., Poole F.L., Shah C., Sugar F.J., Chen C.-Y.,
RA Arendall W.B., Richardson J.S., Richardson D.C., Rose J.P.;
RT "Conserved hypothetical protein Pfu-877259-001 from Pyrococcus furiosus.";
RL Submitted (SEP-2004) to the PDB data bank.
CC -!- FUNCTION: DNA repair enzyme that is part of the base excision repair
CC (BER) pathway; protects from oxidative damage by removing the major
CC product of DNA oxidation, 8-oxoguanine (GO), from single- and double-
CC stranded DNA substrates. {ECO:0000255|HAMAP-Rule:MF_01168}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-
CC deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-
CC dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-
CC 2'-deoxyribonucleoside-DNA + H(+); Xref=Rhea:RHEA:66592, Rhea:RHEA-
CC COMP:13180, Rhea:RHEA-COMP:16897, Rhea:RHEA-COMP:17067,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:136412, ChEBI:CHEBI:157695,
CC ChEBI:CHEBI:167181; EC=4.2.99.18; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01168};
CC -!- DOMAIN: Contains two alpha-helical subdomains, with the 8-oxoguanine
CC binding site located in a cleft at their interface. Contains a helix-
CC hairpin-helix (HhH) structural motif and a Gly/Pro-rich sequence
CC followed by a conserved Asp (HhH-GPD motif).
CC -!- SIMILARITY: Belongs to the archaeal N-glycosylase/DNA lyase (AGOG)
CC family. {ECO:0000255|HAMAP-Rule:MF_01168}.
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DR EMBL; AE009950; AAL81028.1; -; Genomic_DNA.
DR RefSeq; WP_014835272.1; NZ_CP023154.1.
DR PDB; 1XG7; X-ray; 1.88 A; A/B=2-242.
DR PDB; 4PII; X-ray; 2.17 A; A=2-242.
DR PDBsum; 1XG7; -.
DR PDBsum; 4PII; -.
DR AlphaFoldDB; Q8U2D5; -.
DR SMR; Q8U2D5; -.
DR STRING; 186497.PF0904; -.
DR EnsemblBacteria; AAL81028; AAL81028; PF0904.
DR GeneID; 41712714; -.
DR KEGG; pfu:PF0904; -.
DR PATRIC; fig|186497.12.peg.959; -.
DR eggNOG; arCOG04144; Archaea.
DR HOGENOM; CLU_085935_0_0_2; -.
DR OMA; VKMFGYA; -.
DR OrthoDB; 108705at2157; -.
DR PhylomeDB; Q8U2D5; -.
DR EvolutionaryTrace; Q8U2D5; -.
DR Proteomes; UP000001013; Chromosome.
DR GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) endonuclease activity; IEA:UniProtKB-EC.
DR GO; GO:0000702; F:oxidized base lesion DNA N-glycosylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006284; P:base-excision repair; IEA:UniProtKB-UniRule.
DR HAMAP; MF_01168; AGOG; 1.
DR InterPro; IPR016544; AGOG.
DR InterPro; IPR015254; AGOG-like.
DR InterPro; IPR011257; DNA_glycosylase.
DR Pfam; PF09171; AGOG; 1.
DR PIRSF; PIRSF008955; AGOG; 1.
DR SUPFAM; SSF48150; SSF48150; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA damage; DNA excision; DNA repair; Hydrolase; Lyase;
KW Reference proteome.
FT CHAIN 1..242
FT /note="N-glycosylase/DNA lyase"
FT /id="PRO_0000185114"
FT REGION 120..184
FT /note="Helix-hairpin-helix"
FT ACT_SITE 144
FT /note="Schiff-base intermediate with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01168"
FT ACT_SITE 176
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01168"
FT BINDING 26
FT /ligand="8-oxoguanine"
FT /ligand_id="ChEBI:CHEBI:52617"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01168"
FT BINDING 53
FT /ligand="8-oxoguanine"
FT /ligand_id="ChEBI:CHEBI:52617"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01168"
FT BINDING 64
FT /ligand="8-oxoguanine"
FT /ligand_id="ChEBI:CHEBI:52617"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01168"
FT BINDING 148
FT /ligand="8-oxoguanine"
FT /ligand_id="ChEBI:CHEBI:52617"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01168"
FT BINDING 174
FT /ligand="8-oxoguanine"
FT /ligand_id="ChEBI:CHEBI:52617"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01168"
FT BINDING 210
FT /ligand="8-oxoguanine"
FT /ligand_id="ChEBI:CHEBI:52617"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01168"
FT BINDING 214
FT /ligand="8-oxoguanine"
FT /ligand_id="ChEBI:CHEBI:52617"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01168"
FT HELIX 2..22
FT /evidence="ECO:0007829|PDB:1XG7"
FT HELIX 25..34
FT /evidence="ECO:0007829|PDB:1XG7"
FT HELIX 39..51
FT /evidence="ECO:0007829|PDB:1XG7"
FT HELIX 60..71
FT /evidence="ECO:0007829|PDB:1XG7"
FT HELIX 79..86
FT /evidence="ECO:0007829|PDB:1XG7"
FT TURN 87..89
FT /evidence="ECO:0007829|PDB:1XG7"
FT HELIX 97..112
FT /evidence="ECO:0007829|PDB:1XG7"
FT HELIX 116..124
FT /evidence="ECO:0007829|PDB:1XG7"
FT HELIX 126..137
FT /evidence="ECO:0007829|PDB:1XG7"
FT HELIX 144..160
FT /evidence="ECO:0007829|PDB:1XG7"
FT HELIX 177..184
FT /evidence="ECO:0007829|PDB:1XG7"
FT HELIX 191..202
FT /evidence="ECO:0007829|PDB:1XG7"
FT HELIX 206..217
FT /evidence="ECO:0007829|PDB:1XG7"
FT HELIX 227..239
FT /evidence="ECO:0007829|PDB:1XG7"
SQ SEQUENCE 242 AA; 28345 MW; 6FA190D348D3E823 CRC64;
MRELVEIIKG IGIEGAKEVE EKVDRQFYAL QYLFRHQDPE MFIKLVIANS LVSYQLTGRG
EDWWWEFARY FSGREVDSIW KAYGEFLPKS KNNRRLIEAK LNRIRKVEGF LSTLTLKDLE
GYYKNMKMLW KALIKIMGSR EDSKTIVFTV KMFGYASRIA FSRFIPYPME IPIPEDLRIK
SVTSKLTQEK PTKFWMKIGQ ESGVPPLHID SLIWPLLGNA DLTPLDIELR NKLMKLTELL
GL
