KIPN_BPT4
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 03-AUG-2022, entry version 127.
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 Caudovirales; Myoviridae; 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},
RC GT7 {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.
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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 PRIDE; P06855; -.
DR GeneID; 1258796; -.
DR KEGG; vg:1258796; -.
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; Genome.
DR Proteomes; UP000009087; Genome.
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:0047846; F:deoxynucleotide 3'-phosphatase activity; IDA:UniProtKB.
DR GO; GO:0046404; F:polydeoxyribonucleotide 5'-hydroxyl-kinase activity; IEA:UniProtKB-EC.
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; -; 1.
DR Gene3D; 3.40.50.300; -; 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 SFLD; SFLDG00010; C1.8:_polynucleotide_5'-hydrox; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR SUPFAM; SSF56784; SSF56784; 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