NFI_BACSU
ID NFI_BACSU Reviewed; 238 AA.
AC P96724; Q795B8;
DT 07-DEC-2004, integrated into UniProtKB/Swiss-Prot.
DT 28-JUL-2009, sequence version 2.
DT 03-AUG-2022, entry version 111.
DE RecName: Full=Endonuclease V {ECO:0000255|HAMAP-Rule:MF_00801};
DE EC=3.1.21.7 {ECO:0000255|HAMAP-Rule:MF_00801};
DE AltName: Full=Deoxyinosine 3'endonuclease {ECO:0000255|HAMAP-Rule:MF_00801};
DE AltName: Full=Deoxyribonuclease V {ECO:0000255|HAMAP-Rule:MF_00801};
DE Short=DNase V {ECO:0000255|HAMAP-Rule:MF_00801};
GN Name=nfi {ECO:0000255|HAMAP-Rule:MF_00801}; Synonyms=ywqL;
GN OrderedLocusNames=BSU36170;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9353933; DOI=10.1099/00221287-143-10-3313;
RA Presecan E., Moszer I., Boursier L., Cruz Ramos H., De La Fuente V.,
RA Hullo M.-F., Lelong C., Schleich S., Sekowska A., Song B.H., Villani G.,
RA Kunst F., Danchin A., Glaser P.;
RT "The Bacillus subtilis genome from gerBC (311 degrees) to licR (334
RT degrees).";
RL Microbiology 143:3313-3328(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP SEQUENCE REVISION TO 42.
RX PubMed=19383706; DOI=10.1099/mic.0.027839-0;
RA Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A.,
RA Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.;
RT "From a consortium sequence to a unified sequence: the Bacillus subtilis
RT 168 reference genome a decade later.";
RL Microbiology 155:1758-1775(2009).
RN [4]
RP DISRUPTION PHENOTYPE.
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RX PubMed=34280190; DOI=10.1371/journal.pgen.1009682;
RA Kobayashi K.;
RT "Diverse LXG toxin and antitoxin systems specifically mediate intraspecies
RT competition in Bacillus subtilis biofilms.";
RL PLoS Genet. 17:e1009682-e1009682(2021).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
RG Northeast structural genomics consortium (NESG);
RT "Crystal structure of the endonuclease V (BSU36170) from Bacillus subtilis,
RT Northeast structural genomics consortium target SR624.";
RL Submitted (FEB-2009) to the PDB data bank.
CC -!- FUNCTION: DNA repair enzyme involved in the repair of deaminated bases.
CC Selectively cleaves double-stranded DNA at the second phosphodiester
CC bond 3' to a deoxyinosine leaving behind the intact lesion on the
CC nicked DNA. {ECO:0000255|HAMAP-Rule:MF_00801}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage at apurinic or apyrimidinic sites to
CC products with a 5'-phosphate.; EC=3.1.21.7;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00801};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00801};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00801}.
CC -!- DISRUPTION PHENOTYPE: Deletion of the ywqH-ywqI-ywqJ-ywqK-nfi operon
CC has no visible phenotype, however it is out-competed by wild-type
CC cells. {ECO:0000269|PubMed:34280190}.
CC -!- SIMILARITY: Belongs to the endonuclease V family. {ECO:0000255|HAMAP-
CC Rule:MF_00801}.
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DR EMBL; Z92952; CAB07450.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB15634.2; -; Genomic_DNA.
DR PIR; G70067; G70067.
DR RefSeq; NP_391498.2; NC_000964.3.
DR RefSeq; WP_003243213.1; NZ_JNCM01000034.1.
DR PDB; 3GA2; X-ray; 2.10 A; A=1-238.
DR PDBsum; 3GA2; -.
DR AlphaFoldDB; P96724; -.
DR SMR; P96724; -.
DR STRING; 224308.BSU36170; -.
DR PaxDb; P96724; -.
DR PRIDE; P96724; -.
DR EnsemblBacteria; CAB15634; CAB15634; BSU_36170.
DR GeneID; 936894; -.
DR KEGG; bsu:BSU36170; -.
DR PATRIC; fig|224308.179.peg.3914; -.
DR eggNOG; COG1515; Bacteria.
DR InParanoid; P96724; -.
DR OMA; RIHFRQA; -.
DR PhylomeDB; P96724; -.
DR BioCyc; BSUB:BSU36170-MON; -.
DR EvolutionaryTrace; P96724; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0043737; F:deoxyribonuclease V activity; IBA:GO_Central.
DR GO; GO:0016891; F:endoribonuclease activity, producing 5'-phosphomonoesters; IBA:GO_Central.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003727; F:single-stranded RNA binding; IBA:GO_Central.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-UniRule.
DR CDD; cd06559; Endonuclease_V; 1.
DR HAMAP; MF_00801; Endonuclease_5; 1.
DR InterPro; IPR007581; Endonuclease-V.
DR PANTHER; PTHR28511; PTHR28511; 1.
DR Pfam; PF04493; Endonuclease_5; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; DNA damage; DNA repair; Endonuclease; Hydrolase;
KW Magnesium; Metal-binding; Nuclease; Reference proteome.
FT CHAIN 1..238
FT /note="Endonuclease V"
FT /id="PRO_0000159658"
FT BINDING 46
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00801"
FT BINDING 116
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00801"
FT SITE 86
FT /note="Interaction with target DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00801"
FT CONFLICT 42
FT /note="C -> G (in Ref. 1; CAB07450)"
FT /evidence="ECO:0000305"
FT HELIX 14..25
FT /evidence="ECO:0007829|PDB:3GA2"
FT HELIX 36..38
FT /evidence="ECO:0007829|PDB:3GA2"
FT STRAND 40..52
FT /evidence="ECO:0007829|PDB:3GA2"
FT STRAND 55..66
FT /evidence="ECO:0007829|PDB:3GA2"
FT TURN 67..69
FT /evidence="ECO:0007829|PDB:3GA2"
FT STRAND 72..81
FT /evidence="ECO:0007829|PDB:3GA2"
FT STRAND 86..89
FT /evidence="ECO:0007829|PDB:3GA2"
FT HELIX 91..94
FT /evidence="ECO:0007829|PDB:3GA2"
FT HELIX 96..105
FT /evidence="ECO:0007829|PDB:3GA2"
FT STRAND 113..117
FT /evidence="ECO:0007829|PDB:3GA2"
FT STRAND 119..122
FT /evidence="ECO:0007829|PDB:3GA2"
FT HELIX 128..136
FT /evidence="ECO:0007829|PDB:3GA2"
FT STRAND 140..146
FT /evidence="ECO:0007829|PDB:3GA2"
FT STRAND 165..170
FT /evidence="ECO:0007829|PDB:3GA2"
FT STRAND 173..179
FT /evidence="ECO:0007829|PDB:3GA2"
FT STRAND 188..196
FT /evidence="ECO:0007829|PDB:3GA2"
FT HELIX 198..207
FT /evidence="ECO:0007829|PDB:3GA2"
FT HELIX 217..235
FT /evidence="ECO:0007829|PDB:3GA2"
SQ SEQUENCE 238 AA; 27023 MW; 87A59F090CF0047F CRC64;
MKVFDVHKFD MKKEQDFLQV QFNLKNRINL SPTIHPDSIN TCAGVDLAYW EQDGEPYGVC
CIIVIDADTK EVIEKVHSMG RISVPYVSGF LAFRELPLII EAAKKLETEP DVFLFDGNGY
LHYNHMGVAT HAAFFLGKPT IGIAKTYLKI KGCDFVTPEI EVGAYTDIII DGEVYGRALR
TRRDVKPIFL SCGNYIDLDS SYQITMSLIN QESRLPIPVR LADLETHVLR TFYQKNHV
