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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
 
 
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