Top Level Name

  ⌊ Superfamily (core) Haloacid Dehalogenase

    ⌊ Subgroup C1.8: polynucleotide 5'-hydroxyl-kinase c-terminal phosphatase like

     ⌊ Family polynucleotide 5'-hydroxyl-kinase c-terminal phosphatase

  ⌊ FunctionalDomain polynucleotide 5'-hydroxyl-kinase c-terminal phosphatase (ID 2320)

Superfamily Assignment Evidence Code(s) ISS
Family Assignment Evidence Code CFM PubMed:12220496
This entry was last updated onNov. 22, 2017

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Enterobacteria phage T4 Taxon ID: 10665 46015542 URP
Enterobacteria phage T4 Taxon ID: 10665 46015523 URP
Enterobacteria phage T4 Taxon ID: 10665 46015454 URP
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Uniprot

Protein NameAccessionEC Number Identifier
Polynucleotide kinase P06855 2.7.1.78 KIPN_BPT4 (Swiss-Prot)

Sequence

Length of Enzyme (full-length): 301 | Length of Functional Domain: 149

1       10        20        30        40        50        60

XKKIILTIGCPGSGKSTWAREFIAKNPGFYNINRDDYRQSIXAHEERDEYKYTKKKEGIV
TGXQFDTAKSILYGGDSVKGVIISDTNLNPERRLAWETFAKEYGWKVEHKVFDVPWTELV
KRNSKRGTKAVPIDVLRSXYKSXREYLGLPVYNGTPGKPKAVIFDVDGTLAKXNGRGPYD
LEKCDTDVINPXVVELSKXYALXGYQIVVVSGRESGTKEDPTKYYRXTRKWVEDIAGVPL
VXQCQREQGDTRKDDVVKEEIFWKHIAPHFDVKLAIDDRTQVVEXWRRIGVECWQVASGD
F
This shows the full-length sequence of the enzyme. The region of the functional domain is highlighted in black letters, while the residual residues are shown in grey. The Superfamily domain, when present, is shown using underlining. In many cases the functional domain is the full-length sequence.
Conserved catalytic residues (as determined by automated alignment to family, subgroup, or superfamily HMMs) are shown with teal highlighting . Conserved catalytic residues which do not matched the Conserved Alignment Residue are shown with maroon highlighting . Information regarding their function can be found in the Conserved Residues section below.
FASTA formatted full-length sequence.
BLAST this sequence against SFLD.
Scan SFLD-HMMs with this sequence.

Conserved Residues
Superfamily CAR This EFD conserves 1/2 Superfamily-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
165 Asp (D) side chain nucleophile: forms covalent intermediate covalent catalysis -- reactant ISS
Subgroup CAR This EFD conserves 7/7 Subgroup-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
165 Asp (D) side chain Mg2+ ligand, nucleophile: attacks phosphate moiety of substrate to form covalent intermediate covalent catalysis -- reactant,
metal ligand -- binding 		IDA PubMed:12220496
167 Asp (D) side chain Mg2+ ligand, binds phosphate moiety of substrate electrostatic stabiliser -- spectator,
metal ligand -- binding 		ICS PubMed:12220496
211 Ser (S) side chain binds phosphate moiety of substrate substrate binding -- binding ICS PubMed:12220496
213 Arg (R) side chain positions D15 steric role -- spectator IDA PubMed:12220496
254 Asp (D) side chain None -- IDA PubMed:12220496
258 Lys (K) side chain binds phosphate moiety of substrate substrate binding -- binding ICS PubMed:12220496
278 Asp (D) side chain Mg2+ ligand metal ligand -- binding ICS PubMed:12220496

Catalyzed Reaction

polynucleotide 5'-hydroxyl-kinase

+ +
5'-dephospho-DNA
16678		 ATP
15422		 5'-phospho-DNA
16149		 ADP
16761

EC: | IntEnz: | Kegg: | BioCyc: | BRENDA: |

Structures

PDB ID Title Molecule Name Number of
EFDs		 Resolution (Å) Mutant? Het group Links
2IA5 T4 Polynucleotide Kinase/Phosphatase With Bound Sulfate And Magnesium. Polynucleotide Kinase 6 2.9 Magnesium Ion
(2 more ⇓) 		CSA • PDB • PDBSum
1RRC T4 Polynucleotide Kinase Bound To 5'-Gtc-3' Ssdna 5'-D(*Gp*Tp*C)-3' • Polynucleotide Kinase 4 2.46 Selenomethionine
(3 more ⇓) 		CSA • PDB • PDBSum
1RC8 T4 Polynucleotide Kinase Bound To 5'-Gtcac-3' Ssdna 5'-D(*Gp*Tp*Cp*Ap*C)-3' • Polynucleotide Kinase 4 2.75 Selenomethionine
(3 more ⇓) 		CSA • PDB • PDBSum
1LTQ Crystal Structure Of T4 Polynucleotide Kinase Polynucleotide Kinase 4 2.33 Selenomethionine
(2 more ⇓) 		CSA • PDB • PDBSum
1RPZ T4 Polynucleotide Kinase Bound To 5'-Tgcac-3' Ssdna 5'-D(*Tp*Gp*Cp*Ap*C)-3' • Polynucleotide Kinase 4 2.9 Selenomethionine
(3 more ⇓) 		CSA • PDB • PDBSum
Percent identity and alignment length from the BLAST match of the Functional Domain sequence to the PDB sequence.
"Yes" indicates that a GI associated with this Functional Domain was mapped to the PDB ID via UniProtKB.

Curation History
Time Change Annotation Old Value New Value
Nov. 3, 2014, 9:26 a.m. update curation agent sbrown setDomainBoundaries.py
EC number assigned by UniProtKB accession ID.