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Endonuclease V (EC 3.1.21.7) (Deoxyinosine 3'endonuclease) (Deoxyribonuclease V) (DNase V)

 NFI_THEMA               Reviewed;         225 AA.
Q9X2H9;
07-DEC-2004, integrated into UniProtKB/Swiss-Prot.
01-NOV-1999, sequence version 1.
28-MAR-2018, entry version 94.
RecName: Full=Endonuclease V {ECO:0000255|HAMAP-Rule:MF_00801};
EC=3.1.21.7 {ECO:0000255|HAMAP-Rule:MF_00801};
AltName: Full=Deoxyinosine 3'endonuclease {ECO:0000255|HAMAP-Rule:MF_00801};
AltName: Full=Deoxyribonuclease V {ECO:0000255|HAMAP-Rule:MF_00801};
Short=DNase V {ECO:0000255|HAMAP-Rule:MF_00801};
Name=nfi {ECO:0000255|HAMAP-Rule:MF_00801}; OrderedLocusNames=TM_1865;
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099).
Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
NCBI_TaxID=243274;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 43589 / MSB8 / DSM 3109 / JCM 10099;
PubMed=10360571; DOI=10.1038/20601;
Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J.,
Haft D.H., Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A.,
McDonald L.A., Utterback T.R., Malek J.A., Linher K.D., Garrett M.M.,
Stewart A.M., Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L.,
Heidelberg J.F., Sutton G.G., Fleischmann R.D., Eisen J.A., White O.,
Salzberg S.L., Smith H.O., Venter J.C., Fraser C.M.;
"Evidence for lateral gene transfer between Archaea and Bacteria from
genome sequence of Thermotoga maritima.";
Nature 399:323-329(1999).
[2]
CATALYTIC ACTIVITY, FUNCTION, COFACTOR, AND MUTAGENESIS OF ASP-43;
TYR-80; ARG-88; GLU-89; ASP-110; HIS-116; HIS-125 AND LYS-139.
PubMed=12081482; DOI=10.1021/bi015960s;
Huang J., Lu J., Barany F., Cao W.;
"Mutational analysis of endonuclease V from Thermotoga maritima.";
Biochemistry 41:8342-8350(2002).
[3]
X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEXES WITH HYPOXANTHINE
LESION SUBSTRATE; DNA AND MAGNESIUM IONS.
PubMed=19136958; DOI=10.1038/nsmb.1538;
Dalhus B., Arvai A.S., Rosnes I., Olsen O.E., Backe P.H., Alseth I.,
Gao H., Cao W., Tainer J.A., Bjoras M.;
"Structures of endonuclease V with DNA reveal initiation of deaminated
adenine repair.";
Nat. Struct. Mol. Biol. 16:138-143(2009).
[4]
X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) OF 1-222.
Utepbergenov D., Cooper D.R., Derewenda U., Derewenda Z.S.;
"Crystal structure of Tm1865, an Endonuclease V from Thermotoga
maritima.";
Submitted (MAY-2009) to the PDB data bank.
-!- FUNCTION: DNA repair enzyme involved in the repair of deaminated
bases. Selectively cleaves double-stranded DNA at the second
phosphodiester bond 3' to a deoxyinosine leaving behind the intact
lesion on the nicked DNA. In vitro, can also cleave single-
stranded substrates with inosine, double-stranded DNA with
apurinic sites, or DNA sites with uracil or a mismatched base.
When present in molar excess, two protein molecules can bind to
the same DNA substrate and effect cleavage of both strands (in
vitro). {ECO:0000255|HAMAP-Rule:MF_00801,
ECO:0000269|PubMed:12081482}.
-!- CATALYTIC ACTIVITY: Endonucleolytic cleavage at apurinic or
apyrimidinic sites to products with a 5'-phosphate.
{ECO:0000255|HAMAP-Rule:MF_00801, ECO:0000269|PubMed:12081482}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000255|HAMAP-Rule:MF_00801,
ECO:0000269|PubMed:12081482};
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00801}.
-!- SIMILARITY: Belongs to the endonuclease V family.
{ECO:0000255|HAMAP-Rule:MF_00801}.
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EMBL; AE000512; AAD36927.1; -; Genomic_DNA.
PIR; B72202; B72202.
RefSeq; NP_229661.1; NC_000853.1.
RefSeq; WP_004082416.1; NZ_CP011107.1.
PDB; 2W35; X-ray; 2.15 A; A/B=1-225.
PDB; 2W36; X-ray; 2.10 A; A/B=1-225.
PDB; 3HD0; X-ray; 2.70 A; A/B/D=1-222.
PDB; 4B20; X-ray; 2.75 A; A/B=1-225.
PDBsum; 2W35; -.
PDBsum; 2W36; -.
PDBsum; 3HD0; -.
PDBsum; 4B20; -.
SMR; Q9X2H9; -.
DIP; DIP-48482N; -.
STRING; 243274.TM1865; -.
EnsemblBacteria; AAD36927; AAD36927; TM_1865.
GeneID; 897801; -.
KEGG; tma:TM1865; -.
eggNOG; ENOG4105Y7X; Bacteria.
eggNOG; COG1515; LUCA.
InParanoid; Q9X2H9; -.
KO; K05982; -.
OMA; CKYRVPE; -.
BRENDA; 3.1.21.7; 6331.
EvolutionaryTrace; Q9X2H9; -.
Proteomes; UP000008183; Chromosome.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0043737; F:deoxyribonuclease V activity; IEA:UniProtKB-EC.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
CDD; cd06559; Endonuclease_V; 1.
HAMAP; MF_00801; Endonuclease_5; 1.
InterPro; IPR007581; Endonuclease-V.
PANTHER; PTHR28511; PTHR28511; 1.
Pfam; PF04493; Endonuclease_5; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; DNA damage; DNA repair;
Endonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
Reference proteome.
CHAIN 1 225 Endonuclease V.
/FTId=PRO_0000159674.
REGION 139 141 Interaction with target DNA.
REGION 214 221 Interaction with target DNA.
METAL 43 43 Magnesium.
METAL 110 110 Magnesium.
SITE 80 80 Interaction with target DNA.
MUTAGEN 43 43 D->A: Complete loss of enzyme activity.
{ECO:0000269|PubMed:12081482}.
MUTAGEN 80 80 Y->A: Reduced affinity for DNA. No effect
on cleavage of DNA containing inosine.
Abolishes cleavage at apurinic sites.
{ECO:0000269|PubMed:12081482}.
MUTAGEN 88 88 R->A: Reduced affinity for DNA. No effect
on cleavage of DNA containing inosine.
Abolishes cleavage at apurinic sites.
{ECO:0000269|PubMed:12081482}.
MUTAGEN 89 89 E->A: Strongly reduced cleavage of DNA
containing inosine.
{ECO:0000269|PubMed:12081482}.
MUTAGEN 105 105 D->A: No effect on cleavage of DNA
containing inosine.
MUTAGEN 110 110 D->A: Complete loss of enzyme activity.
{ECO:0000269|PubMed:12081482}.
MUTAGEN 116 116 H->A: Reduced affinity for DNA. No effect
on cleavage of DNA containing inosine.
Abolishes cleavage at apurinic sites.
{ECO:0000269|PubMed:12081482}.
MUTAGEN 125 125 H->A: No effect on cleavage of DNA
containing inosine.
{ECO:0000269|PubMed:12081482}.
MUTAGEN 139 139 K->A: No effect on DNA binding. No effect
on cleavage of DNA containing inosine.
Strongly reduced cleavage at apurinic
sites. {ECO:0000269|PubMed:12081482}.
HELIX 13 23 {ECO:0000244|PDB:2W36}.
HELIX 24 26 {ECO:0000244|PDB:2W36}.
STRAND 37 48 {ECO:0000244|PDB:2W36}.
STRAND 51 60 {ECO:0000244|PDB:2W36}.
TURN 61 64 {ECO:0000244|PDB:2W36}.
STRAND 65 75 {ECO:0000244|PDB:2W36}.
HELIX 86 97 {ECO:0000244|PDB:2W36}.
STRAND 105 111 {ECO:0000244|PDB:2W36}.
STRAND 113 116 {ECO:0000244|PDB:2W36}.
HELIX 122 130 {ECO:0000244|PDB:2W36}.
STRAND 134 140 {ECO:0000244|PDB:2W36}.
STRAND 143 145 {ECO:0000244|PDB:3HD0}.
STRAND 151 154 {ECO:0000244|PDB:2W36}.
STRAND 156 161 {ECO:0000244|PDB:2W36}.
STRAND 164 170 {ECO:0000244|PDB:2W36}.
STRAND 179 183 {ECO:0000244|PDB:2W36}.
HELIX 189 199 {ECO:0000244|PDB:2W36}.
HELIX 208 220 {ECO:0000244|PDB:2W36}.
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


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