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Protein

Polynucleotide kinase

Gene

pseT

Organism
Enterobacteria phage T4 (Bacteriophage T4)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

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).4 Publications

Catalytic activityi

ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA.
A deoxynucleoside 3'-phosphate + H2O = a deoxynucleoside + phosphate.1 Publication

Cofactori

Mg2+2 Publications

pH dependencei

Optimum pH is 6.1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Kinase, Transferase

Keywords - Biological processi

DNA damage, DNA repair, Evasion of bacteria-mediated translation shutoff by virus, Host-virus interaction

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BRENDAi2.7.1.78. 732.
SABIO-RKP06855.

Names & Taxonomyi

Protein namesi
Recommended name:
Polynucleotide kinase (EC:2.7.1.78)
Short name:
PNK
Alternative name(s):
Deoxynucleotide 3'-phosphatase1 Publication (EC:3.1.3.341 Publication)
Polynucleotide 5'-hydroxyl-kinase
Gene namesi
Name:pseT
OrganismiEnterobacteria phage T4 (Bacteriophage T4)
Taxonomic identifieri10665 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesMyoviridaeTevenvirinaeT4likevirus
Virus hostiEscherichia coli [TaxID: 562]
Proteomesi
  • UP000009087 Componenti: Genome
  • UP000001092 Componenti: Genome

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL5292.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 301301Polynucleotide kinasePRO_0000164949Add
BLAST

Interactioni

Subunit structurei

Homotetramer.

Chemistry

BindingDBiP06855.

Structurei

Secondary structure

1
301
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 86Combined sources
Helixi15 – 2511Combined sources
Beta strandi29 – 324Combined sources
Helixi34 – 418Combined sources
Helixi47 – 493Combined sources
Helixi54 – 7219Combined sources
Helixi75 – 773Combined sources
Beta strandi80 – 834Combined sources
Helixi90 – 10314Combined sources
Beta strandi106 – 1116Combined sources
Helixi116 – 1238Combined sources
Helixi127 – 1293Combined sources
Helixi133 – 14715Combined sources
Beta strandi156 – 1583Combined sources
Beta strandi160 – 1656Combined sources
Turni168 – 1703Combined sources
Helixi181 – 1866Combined sources
Helixi191 – 20212Combined sources
Beta strandi206 – 2116Combined sources
Beta strandi218 – 2203Combined sources
Helixi223 – 23412Combined sources
Beta strandi241 – 2455Combined sources
Helixi254 – 26512Combined sources
Turni266 – 2694Combined sources
Beta strandi271 – 2777Combined sources
Helixi280 – 2889Combined sources
Beta strandi293 – 2953Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1LTQX-ray2.33A1-301[»]
1LY1X-ray2.00A1-181[»]
1RC8X-ray2.75A1-301[»]
1RPZX-ray2.90A1-301[»]
1RRCX-ray2.46A1-301[»]
2IA5X-ray2.90A/B/C/D/E/F/G/H/I/J/K/L1-301[»]
ProteinModelPortaliP06855.
SMRiP06855. Positions 1-300.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP06855.

Family & Domainsi

Family and domain databases

Gene3Di3.40.50.1000. 1 hit.
3.40.50.300. 1 hit.
InterProiIPR023214. HAD-like_dom.
IPR027417. P-loop_NTPase.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
SSF56784. SSF56784. 1 hit.

Sequencei

Sequence statusi: Complete.

P06855-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKIILTIGC PGSGKSTWAR EFIAKNPGFY NINRDDYRQS IMAHEERDEY
60 70 80 90 100
KYTKKKEGIV TGMQFDTAKS ILYGGDSVKG VIISDTNLNP ERRLAWETFA
110 120 130 140 150
KEYGWKVEHK VFDVPWTELV KRNSKRGTKA VPIDVLRSMY KSMREYLGLP
160 170 180 190 200
VYNGTPGKPK AVIFDVDGTL AKMNGRGPYD LEKCDTDVIN PMVVELSKMY
210 220 230 240 250
ALMGYQIVVV SGRESGTKED PTKYYRMTRK WVEDIAGVPL VMQCQREQGD
260 270 280 290 300
TRKDDVVKEE IFWKHIAPHF DVKLAIDDRT QVVEMWRRIG VECWQVASGD

F
Length:301
Mass (Da):34,620
Last modified:January 1, 1988 - v1
Checksum:i0EAFB6BA83236D31
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03007 Genomic DNA. Translation: CAA26792.1.
AF158101 Genomic DNA. Translation: AAD42642.1.
HM137666 Genomic DNA. Translation: ADJ39944.1.
KJ477684 Genomic DNA. Translation: AHY83527.1.
KJ477685 Genomic DNA. Translation: AHY83726.1.
KJ477686 Genomic DNA. Translation: AHY83916.1.
PIRiA24642. KIBPP4.
RefSeqiNP_049834.1. NC_000866.4.

Genome annotation databases

GeneIDi1258796.
KEGGivg:1258796.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03007 Genomic DNA. Translation: CAA26792.1.
AF158101 Genomic DNA. Translation: AAD42642.1.
HM137666 Genomic DNA. Translation: ADJ39944.1.
KJ477684 Genomic DNA. Translation: AHY83527.1.
KJ477685 Genomic DNA. Translation: AHY83726.1.
KJ477686 Genomic DNA. Translation: AHY83916.1.
PIRiA24642. KIBPP4.
RefSeqiNP_049834.1. NC_000866.4.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1LTQX-ray2.33A1-301[»]
1LY1X-ray2.00A1-181[»]
1RC8X-ray2.75A1-301[»]
1RPZX-ray2.90A1-301[»]
1RRCX-ray2.46A1-301[»]
2IA5X-ray2.90A/B/C/D/E/F/G/H/I/J/K/L1-301[»]
ProteinModelPortaliP06855.
SMRiP06855. Positions 1-300.
ModBaseiSearch...
MobiDBiSearch...

Chemistry

BindingDBiP06855.
ChEMBLiCHEMBL5292.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1258796.
KEGGivg:1258796.

Enzyme and pathway databases

BRENDAi2.7.1.78. 732.
SABIO-RKP06855.

Miscellaneous databases

EvolutionaryTraceiP06855.

Family and domain databases

Gene3Di3.40.50.1000. 1 hit.
3.40.50.300. 1 hit.
InterProiIPR023214. HAD-like_dom.
IPR027417. P-loop_NTPase.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
SSF56784. SSF56784. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "T4 polynucleotide kinase; cloning of the gene (pseT) and amplification of its product."
    Midgley C.A., Murray N.E.
    EMBO J. 4:2695-2703(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "Genomes of the T4-related bacteriophages as windows on microbial genome evolution."
    Petrov V.M., Ratnayaka S., Nolan J.M., Miller E.S., Karam J.D.
    Virol. J. 7:292-292(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9."
    Bryson A.L., Hwang Y., Sherrill-Mix S., Wu G.D., Lewis J.D., Black L., Clark T.A., Bushman F.D.
    MBio 6:E00648-E00648(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 147Imported, GT7Imported and WildImported.
  5. "The enzymatic cleavage of phosphate termini from polynucleotides."
    Becker A., Hurwitz J.
    J. Biol. Chem. 242:936-950(1967) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  6. "Phosphorylation of nucleic acid by an enzyme from T4 bacteriophage-infected Escherichia coli."
    Richardson C.C.
    Proc. Natl. Acad. Sci. U.S.A. 54:158-165(1965) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, COFACTOR.
  7. "3'-Phosphatase activity in T4 polynucleotide kinase."
    Cameron V., Uhlenbeck O.C.
    Biochemistry 16:5120-5126(1977) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, CATALYTIC ACTIVITY.
  8. "Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA."
    Amitsur M., Levitz R., Kaufmann G.
    EMBO J. 6:2499-2503(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "Structure of a tRNA repair enzyme and molecular biology workhorse: T4 polynucleotide kinase."
    Galburt E.A., Pelletier J., Wilson G., Stoddard B.L.
    Structure 10:1249-1260(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.33 ANGSTROMS).

Entry informationi

Entry nameiKIPN_BPT4
AccessioniPrimary (citable) accession number: P06855
Secondary accession number(s): D9IEQ8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 1, 1988
Last modified: May 11, 2016
This is version 103 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.