ID KIPN_BPT4 Reviewed; 301 AA. AC P06855; D9IEQ8; DT 01-JAN-1988, integrated into UniProtKB/Swiss-Prot. DT 01-JAN-1988, sequence version 1. DT 08-NOV-2023, entry version 132. DE RecName: Full=Polynucleotide kinase; DE Short=PNK; DE EC=2.7.1.78; DE AltName: Full=Deoxynucleotide 3'-phosphatase {ECO:0000303|PubMed:199248}; DE EC=3.1.3.34 {ECO:0000269|PubMed:199248}; DE AltName: Full=Polynucleotide 5'-hydroxyl-kinase; GN Name=pseT; OS Enterobacteria phage T4 (Bacteriophage T4). OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; OC Straboviridae; Tevenvirinae; Tequatrovirus. OX NCBI_TaxID=10665; OH NCBI_TaxID=562; Escherichia coli. RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX PubMed=2996886; DOI=10.1002/j.1460-2075.1985.tb03989.x; RA Midgley C.A., Murray N.E.; RT "T4 polynucleotide kinase; cloning of the gene (pseT) and amplification of RT its product."; RL EMBO J. 4:2695-2703(1985). RN [2] 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 [3] 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 [4] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=147 {ECO:0000312|EMBL:AHY83726.1}, GT7 RC {ECO:0000312|EMBL:AHY83916.1}, and Wild {ECO:0000312|EMBL:AHY83527.1}; 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 [5] RP FUNCTION. RX PubMed=4289819; DOI=10.1016/s0021-9258(18)96215-0; RA Becker A., Hurwitz J.; RT "The enzymatic cleavage of phosphate termini from polynucleotides."; RL J. Biol. Chem. 242:936-950(1967). RN [6] RP FUNCTION, AND COFACTOR. RX PubMed=5323016; DOI=10.1073/pnas.54.1.158; RA Richardson C.C.; RT "Phosphorylation of nucleic acid by an enzyme from T4 bacteriophage- RT infected Escherichia coli."; RL Proc. Natl. Acad. Sci. U.S.A. 54:158-165(1965). RN [7] RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND CATALYTIC ACTIVITY. RX PubMed=199248; DOI=10.1021/bi00642a027; RA Cameron V., Uhlenbeck O.C.; RT "3'-Phosphatase activity in T4 polynucleotide kinase."; RL Biochemistry 16:5120-5126(1977). RN [8] RP FUNCTION. RX PubMed=2444436; DOI=10.1002/j.1460-2075.1987.tb02532.x; RA Amitsur M., Levitz R., Kaufmann G.; RT "Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase RT reprocess the host lysine tRNA."; RL EMBO J. 6:2499-2503(1987). RN [9] RP X-RAY CRYSTALLOGRAPHY (2.33 ANGSTROMS). RX PubMed=12220496; DOI=10.1016/s0969-2126(02)00835-3; RA Galburt E.A., Pelletier J., Wilson G., Stoddard B.L.; RT "Structure of a tRNA repair enzyme and molecular biology workhorse: T4 RT polynucleotide kinase."; RL Structure 10:1249-1260(2002). CC -!- FUNCTION: Acts as a 5'-hydroxyl kinase, a 3'-phosphatase and a 2',3'- CC cyclic phosphodiesterase. Catalyzes the transfer of the terminal CC phosphate of ATP to the 5'-hydroxyl termini of ribo- and CC deoxyribonucleotides. In the presence of ADP the enzyme also catalyzes CC an exchange reaction. In the exchange reaction, an excess ADP causes CC the enzyme to transfer the 5' terminal phosphate from phosphorylated CC DNA to ADP (PubMed:5323016, PubMed:199248). Involved in countering a CC host defense mechanism which activates T4-induced anticodon nuclease CC and shuts off viral translation. The polynucleotide kinase modifies the CC ends of nicked tRNA generated by the antiviral response of the host CC bacteria and facilitates repair by T4 RNA ligase (PubMed:2444436). CC {ECO:0000269|PubMed:199248, ECO:0000269|PubMed:2444436, CC ECO:0000269|PubMed:4289819, ECO:0000269|PubMed:5323016}. CC -!- CATALYTIC ACTIVITY: CC Reaction=a 5'-end dephospho-2'-deoxyribonucleoside-DNA + ATP = a 5'-end CC 5'-monophospho-2'-deoxyribonucleoside-DNA + ADP + H(+); CC Xref=Rhea:RHEA:15669, Rhea:RHEA-COMP:13180, Rhea:RHEA-COMP:13184, CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:136412, CC ChEBI:CHEBI:136416, ChEBI:CHEBI:456216; EC=2.7.1.78; CC -!- CATALYTIC ACTIVITY: CC Reaction=a 2'-deoxyribonucleoside 3'-phosphate + H2O = a 2'- CC deoxyribonucleoside + phosphate; Xref=Rhea:RHEA:10092, CC ChEBI:CHEBI:15377, ChEBI:CHEBI:18274, ChEBI:CHEBI:43474, CC ChEBI:CHEBI:131705; EC=3.1.3.34; CC Evidence={ECO:0000269|PubMed:199248}; CC -!- COFACTOR: CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; CC Evidence={ECO:0000269|PubMed:199248, ECO:0000269|PubMed:5323016}; CC -!- BIOPHYSICOCHEMICAL PROPERTIES: CC pH dependence: CC Optimum pH is 6. {ECO:0000269|PubMed:199248}; CC -!- SUBUNIT: Homotetramer. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; X03007; CAA26792.1; -; Genomic_DNA. DR EMBL; AF158101; AAD42642.1; -; Genomic_DNA. DR EMBL; HM137666; ADJ39944.1; -; Genomic_DNA. DR EMBL; KJ477684; AHY83527.1; -; Genomic_DNA. DR EMBL; KJ477685; AHY83726.1; -; Genomic_DNA. DR EMBL; KJ477686; AHY83916.1; -; Genomic_DNA. DR PIR; A24642; KIBPP4. DR RefSeq; NP_049834.1; NC_000866.4. DR PDB; 1LTQ; X-ray; 2.33 A; A=1-301. DR PDB; 1LY1; X-ray; 2.00 A; A=1-181. DR PDB; 1RC8; X-ray; 2.75 A; A=1-301. DR PDB; 1RPZ; X-ray; 2.90 A; A=1-301. DR PDB; 1RRC; X-ray; 2.46 A; A=1-301. DR PDB; 2IA5; X-ray; 2.90 A; A/B/C/D/E/F/G/H/I/J/K/L=1-301. DR PDB; 5UJ0; X-ray; 2.30 A; A/B=158-301. DR PDBsum; 1LTQ; -. DR PDBsum; 1LY1; -. DR PDBsum; 1RC8; -. DR PDBsum; 1RPZ; -. DR PDBsum; 1RRC; -. DR PDBsum; 2IA5; -. DR PDBsum; 5UJ0; -. DR SMR; P06855; -. DR BindingDB; P06855; -. DR ChEMBL; CHEMBL5292; -. DR GeneID; 1258796; -. DR KEGG; vg:1258796; -. DR OrthoDB; 5906at10239; -. DR BRENDA; 2.7.1.78; 732. DR BRENDA; 3.1.3.32; 732. DR SABIO-RK; P06855; -. DR EvolutionaryTrace; P06855; -. DR PRO; PR:P06855; -. DR Proteomes; UP000001092; Segment. DR Proteomes; UP000009087; Segment. DR Proteomes; UP000185269; Genome. DR Proteomes; UP000185270; Genome. DR Proteomes; UP000185271; Genome. DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW. DR GO; GO:0046404; F:ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity; IEA:RHEA. DR GO; GO:0047846; F:deoxynucleotide 3'-phosphatase activity; IDA:UniProtKB. DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW. DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW. DR CDD; cd07502; HAD_PNKP-C; 1. DR Gene3D; 3.40.50.1000; HAD superfamily/HAD-like; 1. DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1. DR InterPro; IPR036412; HAD-like_sf. DR InterPro; IPR023214; HAD_sf. DR InterPro; IPR027417; P-loop_NTPase. DR InterPro; IPR044493; PNKP_C_HAD. DR Pfam; PF13671; AAA_33; 1. DR SFLD; SFLDG00010; C1.8:_polynucleotide_5'-hydrox; 1. DR SFLD; SFLDS00003; Haloacid_Dehalogenase; 1. DR SUPFAM; SSF56784; HAD-like; 1. DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1. PE 1: Evidence at protein level; KW 3D-structure; ATP-binding; DNA damage; DNA repair; KW Evasion of bacteria-mediated translation shutoff by virus; KW Host-virus interaction; Hydrolase; Kinase; Nucleotide-binding; KW Reference proteome; Transferase. FT CHAIN 1..301 FT /note="Polynucleotide kinase" FT /id="PRO_0000164949" FT STRAND 3..8 FT /evidence="ECO:0007829|PDB:1LY1" FT HELIX 15..25 FT /evidence="ECO:0007829|PDB:1LY1" FT STRAND 29..32 FT /evidence="ECO:0007829|PDB:1LY1" FT HELIX 34..41 FT /evidence="ECO:0007829|PDB:1LY1" FT HELIX 47..49 FT /evidence="ECO:0007829|PDB:1LY1" FT HELIX 54..72 FT /evidence="ECO:0007829|PDB:1LY1" FT HELIX 75..77 FT /evidence="ECO:0007829|PDB:2IA5" FT STRAND 80..83 FT /evidence="ECO:0007829|PDB:1LY1" FT HELIX 90..103 FT /evidence="ECO:0007829|PDB:1LY1" FT STRAND 106..111 FT /evidence="ECO:0007829|PDB:1LY1" FT HELIX 116..123 FT /evidence="ECO:0007829|PDB:1LY1" FT HELIX 127..129 FT /evidence="ECO:0007829|PDB:1LY1" FT HELIX 133..147 FT /evidence="ECO:0007829|PDB:1LY1" FT STRAND 156..158 FT /evidence="ECO:0007829|PDB:1RC8" FT STRAND 160..164 FT /evidence="ECO:0007829|PDB:5UJ0" FT TURN 168..170 FT /evidence="ECO:0007829|PDB:5UJ0" FT HELIX 181..186 FT /evidence="ECO:0007829|PDB:5UJ0" FT HELIX 191..202 FT /evidence="ECO:0007829|PDB:5UJ0" FT STRAND 206..214 FT /evidence="ECO:0007829|PDB:5UJ0" FT STRAND 218..220 FT /evidence="ECO:0007829|PDB:5UJ0" FT HELIX 223..234 FT /evidence="ECO:0007829|PDB:5UJ0" FT STRAND 241..246 FT /evidence="ECO:0007829|PDB:5UJ0" FT HELIX 254..265 FT /evidence="ECO:0007829|PDB:5UJ0" FT TURN 266..269 FT /evidence="ECO:0007829|PDB:5UJ0" FT STRAND 271..278 FT /evidence="ECO:0007829|PDB:5UJ0" FT HELIX 280..288 FT /evidence="ECO:0007829|PDB:5UJ0" FT STRAND 293..295 FT /evidence="ECO:0007829|PDB:5UJ0" SQ 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 //