ID A9BVU9_DELAS Unreviewed; 250 AA.
AC A9BVU9;
DT 15-JAN-2008, integrated into UniProtKB/TrEMBL.
DT 15-JAN-2008, sequence version 1.
DT 27-MAR-2024, entry version 90.
DE RecName: Full=Endonuclease III {ECO:0000256|HAMAP-Rule:MF_00942};
DE EC=4.2.99.18 {ECO:0000256|HAMAP-Rule:MF_00942};
DE AltName: Full=DNA-(apurinic or apyrimidinic site) lyase {ECO:0000256|HAMAP-Rule:MF_00942};
GN Name=nth {ECO:0000256|HAMAP-Rule:MF_00942};
GN OrderedLocusNames=Daci_2824 {ECO:0000313|EMBL:ABX35462.1};
OS Delftia acidovorans (strain DSM 14801 / SPH-1).
OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC Comamonadaceae; Delftia.
OX NCBI_TaxID=398578 {ECO:0000313|EMBL:ABX35462.1, ECO:0000313|Proteomes:UP000000784};
RN [1] {ECO:0000313|EMBL:ABX35462.1, ECO:0000313|Proteomes:UP000000784}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 14801 / SPH-1 {ECO:0000313|Proteomes:UP000000784};
RX PubMed=15240283; DOI=10.1128/AEM.70.7.4053-4063.2004;
RA Schleheck D., Knepper T.P., Fischer K., Cook A.M.;
RT "Mineralization of individual congeners of linear alkylbenzenesulfonate by
RT defined pairs of heterotrophic bacteria.";
RL Appl. Environ. Microbiol. 70:4053-4063(2004).
RN [2] {ECO:0000313|Proteomes:UP000000784}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 14801 / SPH-1 {ECO:0000313|Proteomes:UP000000784};
RA Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E.,
RA Tice H., Pitluck S., Lowry S., Clum A., Schmutz J., Larimer F., Land M.,
RA Hauser L., Kyrpides N., Kim E., Schleheck D., Richardson P.;
RT "Complete sequence of Delftia acidovorans DSM 14801 / SPH-1.";
RL Submitted (NOV-2007) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: DNA repair enzyme that has both DNA N-glycosylase activity
CC and AP-lyase activity. The DNA N-glycosylase activity releases various
CC damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving
CC an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the
CC phosphodiester bond 3' to the AP site by a beta-elimination, leaving a
CC 3'-terminal unsaturated sugar and a product with a terminal 5'-
CC phosphate. {ECO:0000256|HAMAP-Rule:MF_00942}.
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:0000256|HAMAP-
CC Rule:MF_00942};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00942};
CC Note=Binds 1 [4Fe-4S] cluster. {ECO:0000256|HAMAP-Rule:MF_00942};
CC -!- SIMILARITY: Belongs to the Nth/MutY family.
CC {ECO:0000256|ARBA:ARBA00008343, ECO:0000256|HAMAP-Rule:MF_00942}.
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DR EMBL; CP000884; ABX35462.1; -; Genomic_DNA.
DR AlphaFoldDB; A9BVU9; -.
DR STRING; 398578.Daci_2824; -.
DR KEGG; dac:Daci_2824; -.
DR eggNOG; COG0177; Bacteria.
DR HOGENOM; CLU_012862_3_0_4; -.
DR Proteomes; UP000000784; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-UniRule.
DR GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) endonuclease activity; IEA:UniProtKB-EC.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0019104; F:DNA N-glycosylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006284; P:base-excision repair; IEA:InterPro.
DR CDD; cd00056; ENDO3c; 1.
DR Gene3D; 1.10.1670.10; Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal); 1.
DR HAMAP; MF_00942; Nth; 1.
DR InterPro; IPR011257; DNA_glycosylase.
DR InterPro; IPR004036; Endonuclease-III-like_CS2.
DR InterPro; IPR003651; Endonuclease3_FeS-loop_motif.
DR InterPro; IPR004035; Endouclease-III_FeS-bd_BS.
DR InterPro; IPR003265; HhH-GPD_domain.
DR InterPro; IPR023170; HhH_base_excis_C.
DR InterPro; IPR000445; HhH_motif.
DR InterPro; IPR005759; Nth.
DR NCBIfam; TIGR01083; nth; 1.
DR PANTHER; PTHR10359; A/G-SPECIFIC ADENINE GLYCOSYLASE/ENDONUCLEASE III; 1.
DR PANTHER; PTHR10359:SF18; ENDONUCLEASE III; 1.
DR Pfam; PF10576; EndIII_4Fe-2S; 1.
DR Pfam; PF00633; HHH; 1.
DR Pfam; PF00730; HhH-GPD; 1.
DR SMART; SM00478; ENDO3c; 1.
DR SMART; SM00525; FES; 1.
DR SUPFAM; SSF48150; DNA-glycosylase; 1.
DR PROSITE; PS00764; ENDONUCLEASE_III_1; 1.
DR PROSITE; PS01155; ENDONUCLEASE_III_2; 1.
PE 3: Inferred from homology;
KW 4Fe-4S {ECO:0000256|ARBA:ARBA00022485, ECO:0000256|HAMAP-Rule:MF_00942};
KW DNA damage {ECO:0000256|ARBA:ARBA00022763, ECO:0000256|HAMAP-
KW Rule:MF_00942};
KW DNA repair {ECO:0000256|ARBA:ARBA00023204, ECO:0000256|HAMAP-
KW Rule:MF_00942}; DNA-binding {ECO:0000256|HAMAP-Rule:MF_00942};
KW Endonuclease {ECO:0000313|EMBL:ABX35462.1};
KW Glycosidase {ECO:0000256|ARBA:ARBA00023295, ECO:0000256|HAMAP-
KW Rule:MF_00942};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|HAMAP-Rule:MF_00942};
KW Iron {ECO:0000256|ARBA:ARBA00023004, ECO:0000256|HAMAP-Rule:MF_00942};
KW Iron-sulfur {ECO:0000256|ARBA:ARBA00023014, ECO:0000256|HAMAP-
KW Rule:MF_00942};
KW Lyase {ECO:0000256|HAMAP-Rule:MF_00942, ECO:0000313|EMBL:ABX35462.1};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_00942}; Nuclease {ECO:0000313|EMBL:ABX35462.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000000784}.
FT DOMAIN 71..218
FT /note="HhH-GPD"
FT /evidence="ECO:0000259|SMART:SM00478"
FT BINDING 220
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00942"
FT BINDING 227
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00942"
FT BINDING 230
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00942"
FT BINDING 236
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00942"
SQ SEQUENCE 250 AA; 27564 MW; 2A0C0EACEF6933D0 CRC64;
MKNQNIPRAC HALSNTRACM TMHATSMDTR PPTMKTTSIE PFFATLKAAN PWPQTELEYT
NVFELLSAVL LSAQATDVGV NKATRKLFPV ANTPQAILDL GLEGLEGYIK TIGLYRSKAK
HLMQTCQILV ERHGGQVPRT REELEALPGV GRKTANVVLN VAFGEPTMAV DTHIFRVGNR
TGLAPGKTPL AVEMQLMKRV PPAYAVDSHH WLILLGRYVC QARKPRCWEC VVAPYCDYSP
KTPAPAAGKR
//
