NFI_THEMA
ID NFI_THEMA Reviewed; 225 AA.
AC Q9X2H9;
DT 07-DEC-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 109.
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}; OrderedLocusNames=TM_1865;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [2]
RP CATALYTIC ACTIVITY, FUNCTION, COFACTOR, AND MUTAGENESIS OF ASP-43; TYR-80;
RP ARG-88; GLU-89; ASP-110; HIS-116; HIS-125 AND LYS-139.
RX PubMed=12081482; DOI=10.1021/bi015960s;
RA Huang J., Lu J., Barany F., Cao W.;
RT "Mutational analysis of endonuclease V from Thermotoga maritima.";
RL Biochemistry 41:8342-8350(2002).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEXES WITH HYPOXANTHINE
RP LESION SUBSTRATE; DNA AND MAGNESIUM IONS.
RX PubMed=19136958; DOI=10.1038/nsmb.1538;
RA Dalhus B., Arvai A.S., Rosnes I., Olsen O.E., Backe P.H., Alseth I.,
RA Gao H., Cao W., Tainer J.A., Bjoras M.;
RT "Structures of endonuclease V with DNA reveal initiation of deaminated
RT adenine repair.";
RL Nat. Struct. Mol. Biol. 16:138-143(2009).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) OF 1-222.
RA Utepbergenov D., Cooper D.R., Derewenda U., Derewenda Z.S.;
RT "Crystal structure of Tm1865, an Endonuclease V from Thermotoga maritima.";
RL Submitted (MAY-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. In vitro, can also cleave single-stranded substrates with
CC inosine, double-stranded DNA with apurinic sites, or DNA sites with
CC uracil or a mismatched base. When present in molar excess, two protein
CC molecules can bind to the same DNA substrate and effect cleavage of
CC both strands (in vitro). {ECO:0000255|HAMAP-Rule:MF_00801,
CC ECO:0000269|PubMed:12081482}.
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 ECO:0000269|PubMed:12081482};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00801,
CC ECO:0000269|PubMed:12081482};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00801}.
CC -!- SIMILARITY: Belongs to the endonuclease V family. {ECO:0000255|HAMAP-
CC Rule:MF_00801}.
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DR EMBL; AE000512; AAD36927.1; -; Genomic_DNA.
DR PIR; B72202; B72202.
DR RefSeq; NP_229661.1; NC_000853.1.
DR RefSeq; WP_004082416.1; NZ_CP011107.1.
DR PDB; 2W35; X-ray; 2.15 A; A/B=1-225.
DR PDB; 2W36; X-ray; 2.10 A; A/B=1-225.
DR PDB; 3HD0; X-ray; 2.70 A; A/B/D=1-222.
DR PDB; 4B20; X-ray; 2.75 A; A/B=1-225.
DR PDB; 6OZF; X-ray; 1.80 A; A/B=1-225.
DR PDB; 6OZG; X-ray; 1.93 A; A/B=1-224.
DR PDBsum; 2W35; -.
DR PDBsum; 2W36; -.
DR PDBsum; 3HD0; -.
DR PDBsum; 4B20; -.
DR PDBsum; 6OZF; -.
DR PDBsum; 6OZG; -.
DR AlphaFoldDB; Q9X2H9; -.
DR SMR; Q9X2H9; -.
DR DIP; DIP-48482N; -.
DR STRING; 243274.THEMA_04845; -.
DR EnsemblBacteria; AAD36927; AAD36927; TM_1865.
DR KEGG; tma:TM1865; -.
DR eggNOG; COG1515; Bacteria.
DR InParanoid; Q9X2H9; -.
DR OMA; RIHFRQA; -.
DR OrthoDB; 1681607at2; -.
DR BRENDA; 3.1.21.7; 6331.
DR EvolutionaryTrace; Q9X2H9; -.
DR Proteomes; UP000008183; 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..225
FT /note="Endonuclease V"
FT /id="PRO_0000159674"
FT REGION 139..141
FT /note="Interaction with target DNA"
FT REGION 214..221
FT /note="Interaction with target DNA"
FT BINDING 43
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 110
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT SITE 80
FT /note="Interaction with target DNA"
FT MUTAGEN 43
FT /note="D->A: Complete loss of enzyme activity."
FT /evidence="ECO:0000269|PubMed:12081482"
FT MUTAGEN 80
FT /note="Y->A: Reduced affinity for DNA. No effect on
FT cleavage of DNA containing inosine. Abolishes cleavage at
FT apurinic sites."
FT /evidence="ECO:0000269|PubMed:12081482"
FT MUTAGEN 88
FT /note="R->A: Reduced affinity for DNA. No effect on
FT cleavage of DNA containing inosine. Abolishes cleavage at
FT apurinic sites."
FT /evidence="ECO:0000269|PubMed:12081482"
FT MUTAGEN 89
FT /note="E->A: Strongly reduced cleavage of DNA containing
FT inosine."
FT /evidence="ECO:0000269|PubMed:12081482"
FT MUTAGEN 105
FT /note="D->A: No effect on cleavage of DNA containing
FT inosine."
FT MUTAGEN 110
FT /note="D->A: Complete loss of enzyme activity."
FT /evidence="ECO:0000269|PubMed:12081482"
FT MUTAGEN 116
FT /note="H->A: Reduced affinity for DNA. No effect on
FT cleavage of DNA containing inosine. Abolishes cleavage at
FT apurinic sites."
FT /evidence="ECO:0000269|PubMed:12081482"
FT MUTAGEN 125
FT /note="H->A: No effect on cleavage of DNA containing
FT inosine."
FT /evidence="ECO:0000269|PubMed:12081482"
FT MUTAGEN 139
FT /note="K->A: No effect on DNA binding. No effect on
FT cleavage of DNA containing inosine. Strongly reduced
FT cleavage at apurinic sites."
FT /evidence="ECO:0000269|PubMed:12081482"
FT STRAND 3..5
FT /evidence="ECO:0007829|PDB:6OZF"
FT HELIX 13..23
FT /evidence="ECO:0007829|PDB:6OZF"
FT HELIX 24..26
FT /evidence="ECO:0007829|PDB:6OZF"
FT STRAND 37..48
FT /evidence="ECO:0007829|PDB:6OZF"
FT STRAND 51..60
FT /evidence="ECO:0007829|PDB:6OZF"
FT TURN 61..63
FT /evidence="ECO:0007829|PDB:6OZF"
FT STRAND 66..75
FT /evidence="ECO:0007829|PDB:6OZF"
FT HELIX 85..99
FT /evidence="ECO:0007829|PDB:6OZF"
FT STRAND 105..111
FT /evidence="ECO:0007829|PDB:6OZF"
FT STRAND 113..116
FT /evidence="ECO:0007829|PDB:6OZF"
FT HELIX 122..130
FT /evidence="ECO:0007829|PDB:6OZF"
FT STRAND 134..140
FT /evidence="ECO:0007829|PDB:6OZF"
FT STRAND 143..145
FT /evidence="ECO:0007829|PDB:3HD0"
FT STRAND 151..154
FT /evidence="ECO:0007829|PDB:2W36"
FT STRAND 156..161
FT /evidence="ECO:0007829|PDB:6OZF"
FT STRAND 164..170
FT /evidence="ECO:0007829|PDB:6OZF"
FT STRAND 179..183
FT /evidence="ECO:0007829|PDB:6OZF"
FT HELIX 189..199
FT /evidence="ECO:0007829|PDB:6OZF"
FT HELIX 208..220
FT /evidence="ECO:0007829|PDB:6OZF"
SQ SEQUENCE 225 AA; 25598 MW; 84250E645E410445 CRC64;
MDYRQLHRWD LPPEEAIKVQ NELRKKIKLT PYEGEPEYVA GVDLSFPGKE EGLAVIVVLE
YPSFKILEVV SERGEITFPY IPGLLAFREG PLFLKAWEKL RTKPDVVVFD GQGLAHPRKL
GIASHMGLFI EIPTIGVAKS RLYGTFKMPE DKRCSWSYLY DGEEIIGCVI RTKEGSAPIF
VSPGHLMDVE SSKRLIKAFT LPGRRIPEPT RLAHIYTQRL KKGLF
