END5_BPT4
ID END5_BPT4 Reviewed; 138 AA.
AC P04418; D9IEF4;
DT 13-AUG-1987, integrated into UniProtKB/Swiss-Prot.
DT 13-AUG-1987, sequence version 1.
DT 25-MAY-2022, entry version 131.
DE RecName: Full=Endonuclease V {ECO:0000303|PubMed:16916523};
DE EC=3.2.2.17 {ECO:0000269|PubMed:6254991, ECO:0000269|PubMed:8347626};
DE AltName: Full=DNA-(apurinic or apyrimidinic site) lyase;
DE Short=AP lyase;
DE EC=4.2.99.18 {ECO:0000269|PubMed:6254991, ECO:0000269|PubMed:8347626};
DE AltName: Full=T4 pyrimidine dimer glycosylase {ECO:0000303|PubMed:16916523};
DE Short=T4-Pdg {ECO:0000303|PubMed:16916523};
OS Enterobacteria phage T4 (Bacteriophage T4).
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Caudovirales; Myoviridae; Tevenvirinae; Tequatrovirus.
OX NCBI_TaxID=10665;
OH NCBI_TaxID=562; Escherichia coli.
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6095188; DOI=10.1093/nar/12.21.8085;
RA Valerie K., Henderson E.E., Deriel J.K.;
RT "Identification, physical map location and sequence of the denV gene from
RT bacteriophage T4.";
RL Nucleic Acids Res. 12:8085-8096(1984).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3024113; DOI=10.1093/nar/14.21.8637;
RA Valerie K., Stevens J., Lynch M., Henderson E.E., de Riel J.K.;
RT "Nucleotide sequence and analysis of the 58.3 to 65.5-kb early region of
RT bacteriophage T4.";
RL Nucleic Acids Res. 14:8637-8654(1986).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6092716; DOI=10.1128/jvi.52.3.846-856.1984;
RA Radany E.H., Naumovski L., Love J.D., Gutekunst K.A., Hall D.H.,
RA Friedberg E.C.;
RT "Physical mapping and complete nucleotide sequence of the denV gene of
RT bacteriophage T4.";
RL J. Virol. 52:846-856(1984).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=12626685; DOI=10.1128/mmbr.67.1.86-156.2003;
RA Miller E.S., Kutter E., Mosig G., Arisaka F., Kunisawa T., Ruger W.;
RT "Bacteriophage T4 genome.";
RL Microbiol. Mol. Biol. Rev. 67:86-156(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=21029436; DOI=10.1186/1743-422x-7-292;
RA Petrov V.M., Ratnayaka S., Nolan J.M., Miller E.S., Karam J.D.;
RT "Genomes of the T4-related bacteriophages as windows on microbial genome
RT evolution.";
RL Virol. J. 7:292-292(2010).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=147 {ECO:0000312|EMBL:AHY83780.1},
RC GT7 {ECO:0000312|EMBL:AHY83971.1}, and Wild {ECO:0000312|EMBL:AHY83587.1};
RX PubMed=26081634; DOI=10.1128/mbio.00648-15;
RA Bryson A.L., Hwang Y., Sherrill-Mix S., Wu G.D., Lewis J.D., Black L.,
RA Clark T.A., Bushman F.D.;
RT "Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9.";
RL MBio 6:E00648-E00648(2015).
RN [7]
RP MUTAGENESIS OF GLU-11; HIS-16; TYR-21; ARG-22; GLU-23; ARG-26; ARG-40;
RP ARG-42; ARG-68; LYS-86; ASP-87; ARG-117; ASP-119; GLU-120; LYS-121;
RP ARG-125; TYR-129; TYR-132 AND LYS-134.
RX PubMed=1409651; DOI=10.1073/pnas.89.20.9420;
RA Doi T., Recktenwald A., Karaki Y., Kikuchi M., Morikawa K., Ikehara M.,
RA Inaoka T., Hori N., Ohtsuka E.;
RT "Role of the basic amino acid cluster and Glu-23 in pyrimidine dimer
RT glycosylase activity of T4 endonuclease V.";
RL Proc. Natl. Acad. Sci. U.S.A. 89:9420-9424(1992).
RN [8]
RP CATALYTIC ACTIVITY, AND FUNCTION.
RX PubMed=8347626; DOI=10.1021/bi00083a032;
RA Dodson M.L., Schrock R.D. III, Lloyd R.S.;
RT "Evidence for an imino intermediate in the T4 endonuclease V reaction.";
RL Biochemistry 32:8284-8290(1993).
RN [9]
RP MUTAGENESIS OF HIS-16.
RX PubMed=14610082; DOI=10.1074/jbc.m304714200;
RA Meador M.G., Rajagopalan L., Lloyd R.S., Dodson M.L.;
RT "Role of His-16 in turnover of T4 pyrimidine dimer glycosylase.";
RL J. Biol. Chem. 279:3348-3353(2004).
RN [10]
RP CATALYTIC ACTIVITY, AND FUNCTION.
RX PubMed=6254991; DOI=10.1016/s0021-9258(19)70242-7;
RA Gordon L.K., Haseltine W.A.;
RT "Comparison of the cleavage of pyrimidine dimers by the bacteriophage T4
RT and Micrococcus luteus UV-specific endonucleases.";
RL J. Biol. Chem. 255:12047-12050(1980).
RN [11]
RP MUTAGENESIS OF GLU-23.
RX PubMed=1357629; DOI=10.1093/nar/20.18.4761;
RA Hori N., Doi T., Karaki Y., Kikuchi M., Ikehara M., Ohtsuka E.;
RT "Participation of glutamic acid 23 of T4 endonuclease V in the beta-
RT elimination reaction of an abasic site in a synthetic duplex DNA.";
RL Nucleic Acids Res. 20:4761-4764(1992).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
RX PubMed=1575827; DOI=10.1126/science.1575827;
RA Morikawa K., Matsumoto O., Tsujimoto M., Katayanagi K., Ariyoshi M.,
RA Doi T., Ikehara M., Inaoka T., Ohtsuka E.;
RT "X-ray structure of T4 endonuclease V: an excision repair enzyme specific
RT for a pyrimidine dimer.";
RL Science 256:523-526(1992).
RN [13] {ECO:0007744|PDB:1VAS}
RP X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) OF 2-138 IN COMPLEX WITH DNA, AND
RP ACTIVE SITE.
RX PubMed=8521494; DOI=10.1016/0092-8674(95)90190-6;
RA Vassylyev D.G., Kashiwagi T., Mikami Y., Ariyoshi M., Iwai S., Ohtsuka E.,
RA Morikawa K.;
RT "Atomic model of a pyrimidine dimer excision repair enzyme complexed with a
RT DNA substrate: structural basis for damaged DNA recognition.";
RL Cell 83:773-782(1995).
RN [14] {ECO:0007744|PDB:1ENI, ECO:0007744|PDB:1ENJ, ECO:0007744|PDB:1ENK, ECO:0007744|PDB:2END}
RP X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS).
RX PubMed=7783199; DOI=10.1006/jmbi.1995.0302;
RA Morikawa K., Ariyoshi M., Vassylyev D.G., Matsumoto O., Katayanagi K.,
RA Ohtsuka E.;
RT "Crystal structure of a pyrimidine dimer-specific excision repair enzyme
RT from bacteriophage T4: refinement at 1.45 A and X-ray analysis of the three
RT active site mutants.";
RL J. Mol. Biol. 249:360-375(1995).
RN [15] {ECO:0007744|PDB:2FCC}
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 2-138 IN COMPLEX WITH ABASIC
RP SITE-CONTAINING DNA, AND FUNCTION.
RX PubMed=16916523; DOI=10.1016/j.jmb.2006.06.059;
RA Golan G., Zharkov D.O., Grollman A.P., Dodson M.L., McCullough A.K.,
RA Lloyd R.S., Shoham G.;
RT "Structure of T4 pyrimidine dimer glycosylase in a reduced imine covalent
RT complex with abasic site-containing DNA.";
RL J. Mol. Biol. 362:241-258(2006).
CC -!- FUNCTION: Participates in the repair of UV-damaged DNA by excising
CC pyrimidine dimers that are the major UV-lesions (PubMed:6254991). DNA
CC glycosylase activity hydrolyzes the glycosylic bond of the 5'
CC pyrimidine of the dimer (PubMed:6254991). This leaves
CC apurinic/apyrimidic (AP) sites in the DNA. These AP sites are removed
CC by the AP lyase activity which cleaves the intrapyrimidine
CC phosphodiester bond (PubMed:6254991). Catalysis proceeds via a
CC protonated imine covalent intermediate between the alpha-amino group of
CC the N-terminal threonine residue and the C1' of the deoxyribose sugar
CC of the 5' pyrimidine at the dimer site (PubMed:8347626)
CC (PubMed:16916523). {ECO:0000269|PubMed:16916523,
CC ECO:0000269|PubMed:6254991, ECO:0000269|PubMed:8347626}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Cleaves the N-glycosidic bond between the 5'-pyrimidine
CC residue in cyclobutadipyrimidine (in DNA) and the corresponding
CC deoxy-D-ribose residue.; EC=3.2.2.17;
CC Evidence={ECO:0000269|PubMed:6254991, ECO:0000269|PubMed:8347626};
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;
CC Evidence={ECO:0000269|PubMed:6254991, ECO:0000269|PubMed:8347626};
CC -!- SUBUNIT: Monomer.
CC -!- MISCELLANEOUS: Phage T4 deficient in the enzymes are extremely
CC sensitive to UV.
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DR EMBL; X04567; CAA28215.1; -; Genomic_DNA.
DR EMBL; AF158101; AAD42563.1; -; Genomic_DNA.
DR EMBL; HM137666; ADJ39840.1; -; Genomic_DNA.
DR EMBL; KJ477684; AHY83587.1; -; Genomic_DNA.
DR EMBL; KJ477685; AHY83780.1; -; Genomic_DNA.
DR EMBL; KJ477686; AHY83971.1; -; Genomic_DNA.
DR PIR; A93540; NEBPT4.
DR RefSeq; NP_049733.1; NC_000866.4.
DR PDB; 1ENI; X-ray; 2.20 A; A=1-138.
DR PDB; 1ENJ; X-ray; 1.80 A; A=1-138.
DR PDB; 1ENK; X-ray; 2.00 A; A=1-138.
DR PDB; 1VAS; X-ray; 2.75 A; A=2-138.
DR PDB; 2END; X-ray; 1.45 A; A=1-138.
DR PDB; 2FCC; X-ray; 2.30 A; A/B=2-138.
DR PDBsum; 1ENI; -.
DR PDBsum; 1ENJ; -.
DR PDBsum; 1ENK; -.
DR PDBsum; 1VAS; -.
DR PDBsum; 2END; -.
DR PDBsum; 2FCC; -.
DR BMRB; P04418; -.
DR SMR; P04418; -.
DR GeneID; 1258606; -.
DR KEGG; vg:1258606; -.
DR BRENDA; 3.1.25.1; 732.
DR BRENDA; 3.2.2.17; 732.
DR EvolutionaryTrace; P04418; -.
DR Proteomes; UP000001092; Genome.
DR Proteomes; UP000009087; Genome.
DR Proteomes; UP000185269; Genome.
DR Proteomes; UP000185270; Genome.
DR Proteomes; UP000185271; Genome.
DR GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) endonuclease activity; IEA:UniProtKB-EC.
DR GO; GO:0033959; F:deoxyribodipyrimidine endonucleosidase activity; IEA:UniProtKB-EC.
DR GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; IDA:UniProtKB.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0000704; F:pyrimidine dimer DNA N-glycosylase activity; IDA:UniProtKB.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR Gene3D; 1.10.440.10; -; 1.
DR InterPro; IPR004260; Pyr-dimer_DNA_glycosylase.
DR InterPro; IPR021143; Pyr-dimer_DNAGlyclase_EndonucV.
DR InterPro; IPR024796; T4_endonuc_V.
DR Pfam; PF03013; Pyr_excise; 1.
DR PIRSF; PIRSF500103; EndoV; 1.
DR PIRSF; PIRSF001000; PDG_ENDV; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA damage; DNA repair; Endonuclease; Glycosidase; Hydrolase;
KW Lyase; Multifunctional enzyme; Nuclease; Reference proteome.
FT CHAIN 1..138
FT /note="Endonuclease V"
FT /id="PRO_0000164934"
FT ACT_SITE 2
FT /note="Nucleophile; via amide nitrogen"
FT /evidence="ECO:0000269|PubMed:8347626,
FT ECO:0007744|PDB:1VAS"
FT ACT_SITE 23
FT /note="Proton acceptor"
FT /evidence="ECO:0000269|PubMed:8347626,
FT ECO:0007744|PDB:1VAS"
FT SITE 3
FT /note="Substrate binding"
FT /evidence="ECO:0000269|PubMed:1409651,
FT ECO:0000269|PubMed:7783199"
FT SITE 22
FT /note="Substrate binding"
FT /evidence="ECO:0000269|PubMed:1409651"
FT SITE 26
FT /note="Transition state stabilizer"
FT /evidence="ECO:0007744|PDB:1VAS"
FT SITE 117
FT /note="Substrate binding"
FT /evidence="ECO:0000269|PubMed:1409651"
FT SITE 121
FT /note="Substrate binding"
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 3
FT /note="R->K: Complete loss of DNA glycosylase activity."
FT /evidence="ECO:0000305|PubMed:1409651"
FT MUTAGEN 11
FT /note="E->Q: 24% decrease in DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 16
FT /note="H->A: 30% decrease in enzymatic activity."
FT /evidence="ECO:0000269|PubMed:14610082"
FT MUTAGEN 16
FT /note="H->C: 40% decrease in enzymatic activity."
FT /evidence="ECO:0000269|PubMed:14610082"
FT MUTAGEN 16
FT /note="H->D: 60% decrease in enzymatic activity."
FT /evidence="ECO:0000269|PubMed:14610082"
FT MUTAGEN 16
FT /note="H->E: 50% decrease in enzymatic activity."
FT /evidence="ECO:0000269|PubMed:14610082"
FT MUTAGEN 16
FT /note="H->K: 75% decrease in enzymatic activity."
FT /evidence="ECO:0000269|PubMed:14610082"
FT MUTAGEN 16
FT /note="H->Q: 60% decrease in enzymatic activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 16
FT /note="H->S: 70% decrease in enzymatic activity."
FT /evidence="ECO:0000269|PubMed:14610082"
FT MUTAGEN 21
FT /note="Y->F: No effect on DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 22
FT /note="R->Q: Almost complete loss of DNA glycosylase
FT activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 23
FT /note="E->D: Complete loss of DNA glycosylase activity. No
FT effect on AP lyase activity."
FT /evidence="ECO:0000269|PubMed:1357629,
FT ECO:0000269|PubMed:1409651"
FT MUTAGEN 23
FT /note="E->Q: Complete loss of DNA glycosylase activity.
FT Complete loss of AP lyase activity."
FT /evidence="ECO:0000269|PubMed:1357629,
FT ECO:0000269|PubMed:1409651"
FT MUTAGEN 26
FT /note="R->Q: Almost complete loss of DNA glycosylase
FT activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 32
FT /note="R->Q: 10% decrease in DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 40
FT /note="R->Q: 20% decrease in DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 42
FT /note="R->Q: 25% decrease in DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 68
FT /note="R->Q: 35% decrease in DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 86
FT /note="K->Q: No effect on DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 87
FT /note="D->E: No effect on DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 87
FT /note="D->N: 20% decrease in DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 117
FT /note="R->Q: 60% decrease in DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 119
FT /note="D->N: 5% decrease in DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 120
FT /note="E->Q: 10% decrease in DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 121
FT /note="K->Q: 90% decrease in DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 125
FT /note="R->Q: 10% decrease in DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 129
FT /note="Y->F: 65% decrease in DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 132
FT /note="Y->W: 10% decrease in DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT MUTAGEN 134
FT /note="K->Q: 20% decrease in DNA glycosylase activity."
FT /evidence="ECO:0000269|PubMed:1409651"
FT HELIX 9..11
FT /evidence="ECO:0007829|PDB:2END"
FT HELIX 14..23
FT /evidence="ECO:0007829|PDB:2END"
FT HELIX 26..36
FT /evidence="ECO:0007829|PDB:2END"
FT HELIX 41..43
FT /evidence="ECO:0007829|PDB:2END"
FT TURN 54..57
FT /evidence="ECO:0007829|PDB:2END"
FT HELIX 58..60
FT /evidence="ECO:0007829|PDB:2END"
FT HELIX 64..80
FT /evidence="ECO:0007829|PDB:2END"
FT HELIX 98..100
FT /evidence="ECO:0007829|PDB:2END"
FT HELIX 108..124
FT /evidence="ECO:0007829|PDB:2END"
FT HELIX 126..128
FT /evidence="ECO:0007829|PDB:2END"
FT STRAND 131..133
FT /evidence="ECO:0007829|PDB:1ENJ"
SQ SEQUENCE 138 AA; 16079 MW; 90B889C8E6686697 CRC64;
MTRINLTLVS ELADQHLMAE YRELPRVFGA VRKHVANGKR VRDFKISPTF ILGAGHVTFF
YDKLEFLRKR QIELIAECLK RGFNIKDTTV QDISDIPQEF RGDYIPHEAS IAISQARLDE
KIAQRPTWYK YYGKAIYA
