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Polynucleotide kinase (PNK) (EC 2.7.1.78) (Deoxynucleotide 3'-phosphatase) (EC 3.1.3.34) (Polynucleotide 5'-hydroxyl-kinase)

 KIPN_BPT4               Reviewed;         301 AA.
P06855; D9IEQ8;
01-JAN-1988, integrated into UniProtKB/Swiss-Prot.
01-JAN-1988, sequence version 1.
25-OCT-2017, entry version 113.
RecName: Full=Polynucleotide kinase;
Short=PNK;
EC=2.7.1.78;
AltName: Full=Deoxynucleotide 3'-phosphatase {ECO:0000303|PubMed:199248};
EC=3.1.3.34 {ECO:0000269|PubMed:199248};
AltName: Full=Polynucleotide 5'-hydroxyl-kinase;
Name=pseT;
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=2996886;
Midgley C.A., Murray N.E.;
"T4 polynucleotide kinase; cloning of the gene (pseT) and
amplification of its product.";
EMBO J. 4:2695-2703(1985).
[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]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=21029436; DOI=10.1186/1743-422X-7-292;
Petrov V.M., Ratnayaka S., Nolan J.M., Miller E.S., Karam J.D.;
"Genomes of the T4-related bacteriophages as windows on microbial
genome evolution.";
Virol. J. 7:292-292(2010).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=147 {ECO:0000312|EMBL:AHY83726.1},
GT7 {ECO:0000312|EMBL:AHY83916.1}, and
Wild {ECO:0000312|EMBL:AHY83527.1};
PubMed=26081634; DOI=10.1128/mBio.00648-15;
Bryson A.L., Hwang Y., Sherrill-Mix S., Wu G.D., Lewis J.D., Black L.,
Clark T.A., Bushman F.D.;
"Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9.";
MBio 6:E00648-E00648(2015).
[5]
FUNCTION.
PubMed=4289819;
Becker A., Hurwitz J.;
"The enzymatic cleavage of phosphate termini from polynucleotides.";
J. Biol. Chem. 242:936-950(1967).
[6]
FUNCTION, AND COFACTOR.
PubMed=5323016; DOI=10.1073/pnas.54.1.158;
Richardson C.C.;
"Phosphorylation of nucleic acid by an enzyme from T4 bacteriophage-
infected Escherichia coli.";
Proc. Natl. Acad. Sci. U.S.A. 54:158-165(1965).
[7]
FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND CATALYTIC
ACTIVITY.
PubMed=199248; DOI=10.1021/bi00642a027;
Cameron V., Uhlenbeck O.C.;
"3'-Phosphatase activity in T4 polynucleotide kinase.";
Biochemistry 16:5120-5126(1977).
[8]
FUNCTION.
PubMed=2444436;
Amitsur M., Levitz R., Kaufmann G.;
"Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA
ligase reprocess the host lysine tRNA.";
EMBO J. 6:2499-2503(1987).
[9]
X-RAY CRYSTALLOGRAPHY (2.33 ANGSTROMS).
PubMed=12220496; DOI=10.1016/S0969-2126(02)00835-3;
Galburt E.A., Pelletier J., Wilson G., Stoddard B.L.;
"Structure of a tRNA repair enzyme and molecular biology workhorse: T4
polynucleotide kinase.";
Structure 10:1249-1260(2002).
-!- FUNCTION: Acts as a 5'-hydroxyl kinase, a 3'-phosphatase and a
2',3'-cyclic phosphodiesterase. Catalyzes the transfer of the
terminal phosphate of ATP to the 5'-hydroxyl termini of ribo- and
deoxyribonucleotides. In the presence of ADP the enzyme also
catalyzes an exchange reaction. In the exchange reaction, an
excess ADP causes the enzyme to transfer the 5' terminal phosphate
from phosphorylated DNA to ADP (PubMed:5323016, PubMed:199248).
Involved in countering a host defense mechanism which activates
T4-induced anticodon nuclease and shuts off viral translation. The
polynucleotide kinase modifies the ends of nicked tRNA generated
by the antiviral response of the host bacteria and facilitates
repair by T4 RNA ligase (PubMed:2444436).
{ECO:0000269|PubMed:199248, ECO:0000269|PubMed:2444436,
ECO:0000269|PubMed:4289819, ECO:0000269|PubMed:5323016}.
-!- CATALYTIC ACTIVITY: ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA.
-!- CATALYTIC ACTIVITY: A deoxyribonucleoside 3'-phosphate + H(2)O = a
deoxyribonucleoside + phosphate. {ECO:0000269|PubMed:199248}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:199248,
ECO:0000269|PubMed:5323016};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
pH dependence:
Optimum pH is 6. {ECO:0000269|PubMed:199248};
-!- SUBUNIT: Homotetramer.
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EMBL; X03007; CAA26792.1; -; Genomic_DNA.
EMBL; AF158101; AAD42642.1; -; Genomic_DNA.
EMBL; HM137666; ADJ39944.1; -; Genomic_DNA.
EMBL; KJ477684; AHY83527.1; -; Genomic_DNA.
EMBL; KJ477685; AHY83726.1; -; Genomic_DNA.
EMBL; KJ477686; AHY83916.1; -; Genomic_DNA.
PIR; A24642; KIBPP4.
RefSeq; NP_049834.1; NC_000866.4.
PDB; 1LTQ; X-ray; 2.33 A; A=1-301.
PDB; 1LY1; X-ray; 2.00 A; A=1-181.
PDB; 1RC8; X-ray; 2.75 A; A=1-301.
PDB; 1RPZ; X-ray; 2.90 A; A=1-301.
PDB; 1RRC; X-ray; 2.46 A; A=1-301.
PDB; 2IA5; X-ray; 2.90 A; A/B/C/D/E/F/G/H/I/J/K/L=1-301.
PDB; 5UJ0; X-ray; 2.30 A; A/B=158-301.
PDBsum; 1LTQ; -.
PDBsum; 1LY1; -.
PDBsum; 1RC8; -.
PDBsum; 1RPZ; -.
PDBsum; 1RRC; -.
PDBsum; 2IA5; -.
PDBsum; 5UJ0; -.
ProteinModelPortal; P06855; -.
SMR; P06855; -.
BindingDB; P06855; -.
ChEMBL; CHEMBL5292; -.
GeneID; 1258796; -.
KEGG; vg:1258796; -.
OrthoDB; VOG0900002N; -.
BRENDA; 2.7.1.78; 732.
SABIO-RK; P06855; -.
EvolutionaryTrace; P06855; -.
PRO; PR:P06855; -.
Proteomes; UP000001092; Genome.
Proteomes; UP000009087; Genome.
Proteomes; UP000185269; Genome.
Proteomes; UP000185270; Genome.
Proteomes; UP000185271; Genome.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0046404; F:ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity; IEA:UniProtKB-EC.
GO; GO:0047846; F:deoxynucleotide 3'-phosphatase activity; IDA:UniProtKB.
GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
GO; GO:0016032; P:viral process; IEA:UniProtKB-KW.
Gene3D; 3.40.50.1000; -; 1.
InterPro; IPR036412; HAD-like_sf.
InterPro; IPR023214; HAD_sf.
InterPro; IPR027417; P-loop_NTPase.
SUPFAM; SSF52540; SSF52540; 1.
SUPFAM; SSF56784; SSF56784; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Complete proteome; DNA damage; DNA repair;
Evasion of bacteria-mediated translation shutoff by virus;
Host-virus interaction; Hydrolase; Kinase; Nucleotide-binding;
Reference proteome; Transferase.
CHAIN 1 301 Polynucleotide kinase.
/FTId=PRO_0000164949.
STRAND 3 8 {ECO:0000244|PDB:1LY1}.
HELIX 15 25 {ECO:0000244|PDB:1LY1}.
STRAND 29 32 {ECO:0000244|PDB:1LY1}.
HELIX 34 41 {ECO:0000244|PDB:1LY1}.
HELIX 47 49 {ECO:0000244|PDB:1LY1}.
HELIX 54 72 {ECO:0000244|PDB:1LY1}.
HELIX 75 77 {ECO:0000244|PDB:2IA5}.
STRAND 80 83 {ECO:0000244|PDB:1LY1}.
HELIX 90 103 {ECO:0000244|PDB:1LY1}.
STRAND 106 111 {ECO:0000244|PDB:1LY1}.
HELIX 116 123 {ECO:0000244|PDB:1LY1}.
HELIX 127 129 {ECO:0000244|PDB:1LY1}.
HELIX 133 147 {ECO:0000244|PDB:1LY1}.
STRAND 156 158 {ECO:0000244|PDB:1RC8}.
STRAND 160 164 {ECO:0000244|PDB:5UJ0}.
TURN 168 170 {ECO:0000244|PDB:5UJ0}.
HELIX 181 186 {ECO:0000244|PDB:5UJ0}.
HELIX 191 202 {ECO:0000244|PDB:5UJ0}.
STRAND 206 214 {ECO:0000244|PDB:5UJ0}.
STRAND 218 220 {ECO:0000244|PDB:5UJ0}.
HELIX 223 234 {ECO:0000244|PDB:5UJ0}.
STRAND 241 246 {ECO:0000244|PDB:5UJ0}.
HELIX 254 265 {ECO:0000244|PDB:5UJ0}.
TURN 266 269 {ECO:0000244|PDB:5UJ0}.
STRAND 271 278 {ECO:0000244|PDB:5UJ0}.
HELIX 280 288 {ECO:0000244|PDB:5UJ0}.
STRAND 293 295 {ECO:0000244|PDB:5UJ0}.
SEQUENCE 301 AA; 34620 MW; 0EAFB6BA83236D31 CRC64;
MKKIILTIGC PGSGKSTWAR EFIAKNPGFY NINRDDYRQS IMAHEERDEY KYTKKKEGIV
TGMQFDTAKS ILYGGDSVKG VIISDTNLNP ERRLAWETFA KEYGWKVEHK VFDVPWTELV
KRNSKRGTKA VPIDVLRSMY KSMREYLGLP VYNGTPGKPK AVIFDVDGTL AKMNGRGPYD
LEKCDTDVIN PMVVELSKMY ALMGYQIVVV SGRESGTKED PTKYYRMTRK WVEDIAGVPL
VMQCQREQGD TRKDDVVKEE IFWKHIAPHF DVKLAIDDRT QVVEMWRRIG VECWQVASGD
F


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