ID D7A9C3_STAND Unreviewed; 272 AA.
AC D7A9C3;
DT 10-AUG-2010, integrated into UniProtKB/TrEMBL.
DT 10-AUG-2010, sequence version 1.
DT 24-JAN-2024, entry version 60.
DE SubName: Full=Exodeoxyribonuclease III {ECO:0000313|EMBL:ADH90685.1};
GN OrderedLocusNames=Snov_3411 {ECO:0000313|EMBL:ADH90685.1};
OS Starkeya novella (strain ATCC 8093 / DSM 506 / JCM 20403 / CCM 1077 / IAM
OS 12100 / NBRC 12443 / NCIMB 10456).
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC Xanthobacteraceae; Starkeya.
OX NCBI_TaxID=639283 {ECO:0000313|EMBL:ADH90685.1, ECO:0000313|Proteomes:UP000006633};
RN [1] {ECO:0000313|EMBL:ADH90685.1, ECO:0000313|Proteomes:UP000006633}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 8093 / DSM 506 / JCM 20403 / CCM 1077 / IAM 12100 / NBRC
RC 12443 / NCIMB 10456 {ECO:0000313|Proteomes:UP000006633};
RX PubMed=23450099; DOI=10.4056/sigs.3006378;
RA Kappler U., Davenport K., Beatson S., Lucas S., Lapidus A., Copeland A.,
RA Berry K.W., Glavina Del Rio T., Hammon N., Dalin E., Tice H., Pitluck S.,
RA Richardson P., Bruce D., Goodwin L.A., Han C., Tapia R., Detter J.C.,
RA Chang Y.J., Jeffries C.D., Land M., Hauser L., Kyrpides N.C., Goker M.,
RA Ivanova N., Klenk H.P., Woyke T.;
RT "Complete genome sequence of the facultatively chemolithoautotrophic and
RT methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC
RT 8093(T)).";
RL Stand. Genomic Sci. 7:44-58(2012).
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|PIRSR:PIRSR604808-2};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|PIRSR:PIRSR604808-2};
CC Note=Probably binds two magnesium or manganese ions per subunit.
CC {ECO:0000256|PIRSR:PIRSR604808-2};
CC -!- SIMILARITY: Belongs to the DNA repair enzymes AP/ExoA family.
CC {ECO:0000256|ARBA:ARBA00007092}.
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DR EMBL; CP002026; ADH90685.1; -; Genomic_DNA.
DR RefSeq; WP_013168186.1; NC_014217.1.
DR AlphaFoldDB; D7A9C3; -.
DR STRING; 639283.Snov_3411; -.
DR KEGG; sno:Snov_3411; -.
DR eggNOG; COG0708; Bacteria.
DR HOGENOM; CLU_027539_0_0_5; -.
DR OMA; HTPIEVE; -.
DR OrthoDB; 9803914at2; -.
DR Proteomes; UP000006633; Chromosome.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0008311; F:double-stranded DNA 3'-5' DNA exonuclease activity; IEA:UniProtKB-EC.
DR GO; GO:0004519; F:endonuclease activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IEA:InterPro.
DR CDD; cd09086; ExoIII-like_AP-endo; 1.
DR Gene3D; 3.60.10.10; Endonuclease/exonuclease/phosphatase; 1.
DR InterPro; IPR004808; AP_endonuc_1.
DR InterPro; IPR020847; AP_endonuclease_F1_BS.
DR InterPro; IPR036691; Endo/exonu/phosph_ase_sf.
DR InterPro; IPR005135; Endo/exonuclease/phosphatase.
DR InterPro; IPR037493; ExoIII-like.
DR NCBIfam; TIGR00633; xth; 1.
DR PANTHER; PTHR43250; -; 1.
DR PANTHER; PTHR43250:SF2; EXODEOXYRIBONUCLEASE III; 1.
DR Pfam; PF03372; Exo_endo_phos; 1.
DR SUPFAM; SSF56219; DNase I-like; 1.
DR PROSITE; PS00726; AP_NUCLEASE_F1_1; 1.
DR PROSITE; PS51435; AP_NUCLEASE_F1_4; 1.
PE 3: Inferred from homology;
KW Magnesium {ECO:0000256|PIRSR:PIRSR604808-2};
KW Manganese {ECO:0000256|PIRSR:PIRSR604808-2};
KW Metal-binding {ECO:0000256|PIRSR:PIRSR604808-2}.
FT DOMAIN 6..263
FT /note="Endonuclease/exonuclease/phosphatase"
FT /evidence="ECO:0000259|Pfam:PF03372"
FT ACT_SITE 113
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-1"
FT ACT_SITE 159
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-1"
FT ACT_SITE 263
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-1"
FT BINDING 9
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-2"
FT BINDING 36
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-2"
FT BINDING 159
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-2"
FT BINDING 161
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-2"
FT BINDING 262
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-2"
FT BINDING 263
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-2"
FT SITE 161
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-3"
FT SITE 233
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-3"
FT SITE 263
FT /note="Interaction with DNA substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR604808-3"
SQ SEQUENCE 272 AA; 30769 MW; D603D3582D019E5D CRC64;
MPLTIATWNI NSVRLRIGLV EKLAAEYQPD VICLQETKTP DDRFPLKDAA KFGYPHAAIH
GQKGYHGVAI LSKRPFDQVS RQGFCDIGDA RHICVTLGRE AGLEAPLTIH NFYIPAGGDI
PDPALNEKFR HKLAFLDEAT MWEQLHPEDP TARSVLVGDL NIAPLETDVW SHKQLLDVVS
HTPIEVEKLE KLQAAGRWVD VMRNFVPPDE RLYTWWSYRA ADWEASNRGR RLDHVWATPA
FAPTARAMNV VRAARSWERP SDHVPVVVTF DV
//