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Endonuclease II (EC 3.1.21.8)

 END2_BPT4               Reviewed;         136 AA.
P07059;
01-APR-1988, integrated into UniProtKB/Swiss-Prot.
03-SEP-2014, sequence version 3.
25-OCT-2017, entry version 86.
RecName: Full=Endonuclease II;
EC=3.1.21.8 {ECO:0000269|PubMed:18539732, ECO:0000269|PubMed:19666720, ECO:0000269|PubMed:6887350, ECO:0000269|PubMed:8386173};
Name=denA;
Enterobacteria phage T4 (Bacteriophage T4).
Viruses; dsDNA viruses, no RNA stage; Caudovirales; Myoviridae;
Tevenvirinae; T4virus.
NCBI_TaxID=10665;
NCBI_TaxID=562; Escherichia coli.
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=3530746;
Sjoeberg B.-M., Hahne S., Mathews C.Z., Mathews C.K., Rand K.N.,
Gait M.J.;
"The bacteriophage T4 gene for the small subunit of ribonucleotide
reductase contains an intron.";
EMBO J. 5:2031-2036(1986).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=12626685; DOI=10.1128/MMBR.67.1.86-156.2003;
Miller E.S., Kutter E., Mosig G., Arisaka F., Kunisawa T., Ruger W.;
"Bacteriophage T4 genome.";
Microbiol. Mol. Biol. Rev. 67:86-156(2003).
[3]
FUNCTION IN HOST DNA DEGRADATION, AND CATALYTIC ACTIVITY.
PubMed=6887350;
Carlson K., Wiberg J.S.;
"In vivo cleavage of cytosine-containing bacteriophage T4 DNA to
genetically distinct, discretely sized fragments.";
J. Virol. 48:18-30(1983).
[4]
FUNCTION, AND CATALYTIC ACTIVITY.
PubMed=8386173;
Carlson K., Krabbe M., Nystroem A.C., Kosturko L.D.;
"DNA determinants of restriction. Bacteriophage T4 endonuclease II-
dependent cleavage of plasmid DNA in vivo.";
J. Biol. Chem. 268:8908-8918(1993).
[5]
FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND MUTAGENESIS OF GLY-49;
ARG-57; LEU-84 AND GLU-118.
PubMed=18539732; DOI=10.1128/JB.00094-08;
Lagerbaeck P., Carlson K.;
"Amino acid residues in the GIY-YIG endonuclease II of phage T4
affecting sequence recognition and binding as well as catalysis.";
J. Bacteriol. 190:5533-5544(2008).
[6]
SUBUNIT, CATALYTIC ACTIVITY, FUNCTION, AND DNA-BINDING.
PubMed=19666720; DOI=10.1093/nar/gkp652;
Lagerback P., Andersson E., Malmberg C., Carlson K.;
"Bacteriophage T4 endonuclease II, a promiscuous GIY-YIG nuclease,
binds as a tetramer to two DNA substrates.";
Nucleic Acids Res. 37:6174-6183(2009).
[7]
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), AND SUBUNIT.
PubMed=20156453; DOI=10.1016/j.jmb.2010.01.076;
Andersson C.E., Lagerback P., Carlson K.;
"Structure of bacteriophage T4 endonuclease II mutant E118A, a
tetrameric GIY-YIG enzyme.";
J. Mol. Biol. 397:1003-1016(2010).
-!- FUNCTION: Contributes to the degradation of host DNA, permitting
the scavenging of host-derived nucleotides for phage DNA synthesis
(PubMed:19666720, PubMed:18539732). Sequence-specific
endonuclease. Catalyzes nicking of the bottom strand of double-
stranded DNA between the first and second base pair to the right
of a top-strand CCGC motif. Does not cleave native phage DNA,
which contains 5-hydroxymethylcytosine instead of cytosine.
{ECO:0000269|PubMed:18539732, ECO:0000269|PubMed:6887350,
ECO:0000269|PubMed:8386173, ECO:0000303|PubMed:18539732,
ECO:0000303|PubMed:19666720}.
-!- CATALYTIC ACTIVITY: Endonucleolytic nicking and cleavage of
cytosine-containing double-stranded DNA.
{ECO:0000269|PubMed:18539732, ECO:0000269|PubMed:19666720,
ECO:0000269|PubMed:6887350, ECO:0000269|PubMed:8386173}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:18539732};
-!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:19666720,
ECO:0000269|PubMed:20156453}.
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EMBL; X04140; CAA27759.1; -; Genomic_DNA.
EMBL; AF158101; AAD42558.1; -; Genomic_DNA.
PIR; S08603; ZNBPT4.
RefSeq; NP_049840.1; NC_000866.4.
PDB; 2WSH; X-ray; 1.90 A; A/B/C/D=1-136.
PDBsum; 2WSH; -.
SMR; P07059; -.
GeneID; 1258710; -.
KEGG; vg:1258710; -.
KO; K20841; -.
OrthoDB; VOG0900010F; -.
BRENDA; 3.1.21.8; 732.
EvolutionaryTrace; P07059; -.
Proteomes; UP000009087; Genome.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0099015; P:degradation of host chromosome by virus; IEA:UniProtKB-KW.
GO; GO:0039657; P:suppression by virus of host gene expression; IEA:UniProtKB-KW.
Gene3D; 3.40.1440.10; -; 1.
InterPro; IPR000305; GIY-YIG_endonuc.
InterPro; IPR035901; GIY-YIG_endonuc_sf.
InterPro; IPR016413; Phage_T4_DenA_endoDNaseII.
Pfam; PF01541; GIY-YIG; 1.
PIRSF; PIRSF004362; Endonuclease_II_phage_DenA; 1.
SMART; SM00465; GIYc; 1.
SUPFAM; SSF82771; SSF82771; 1.
PROSITE; PS50164; GIY_YIG; 1.
1: Evidence at protein level;
3D-structure; Bacterial host gene expression shutoff by virus;
Complete proteome; Degradation of host chromosome by virus;
DNA-binding; Endonuclease; Host gene expression shutoff by virus;
Host-virus interaction; Hydrolase; Magnesium; Metal-binding; Nuclease;
Reference proteome.
CHAIN 1 136 Endonuclease II.
/FTId=PRO_0000164932.
DOMAIN 32 131 GIY-YIG. {ECO:0000255|PROSITE-
ProRule:PRU00977}.
MUTAGEN 49 49 G->A: Nearly abolishes endonuclease
activity. {ECO:0000269|PubMed:18539732}.
MUTAGEN 57 57 R->A: Nearly abolishes endonuclease
activity. {ECO:0000269|PubMed:18539732}.
MUTAGEN 84 84 L->P: Nearly abolishes endonuclease
activity. {ECO:0000269|PubMed:18539732}.
MUTAGEN 118 118 E->A: Abolishes endonuclease activity.
{ECO:0000269|PubMed:18539732}.
HELIX 1 7 {ECO:0000244|PDB:2WSH}.
STRAND 11 16 {ECO:0000244|PDB:2WSH}.
STRAND 34 41 {ECO:0000244|PDB:2WSH}.
STRAND 44 52 {ECO:0000244|PDB:2WSH}.
HELIX 54 66 {ECO:0000244|PDB:2WSH}.
HELIX 75 85 {ECO:0000244|PDB:2WSH}.
STRAND 90 96 {ECO:0000244|PDB:2WSH}.
STRAND 99 104 {ECO:0000244|PDB:2WSH}.
STRAND 107 112 {ECO:0000244|PDB:2WSH}.
HELIX 114 125 {ECO:0000244|PDB:2WSH}.
SEQUENCE 136 AA; 15802 MW; 223499122C6EF8BB CRC64;
MKEIATEYSF IKYTELELDD NGSIKQLSIP NKYNVIYAIA INDELVYIGK TKNLRKRINY
YRTAINRKDK TSDSTKSALI HSALKEGSKV EFYARQCFNL SMTNELGTMT IATIDLEEPL
FIKLFNPPWN IQHKKK


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