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(-) Description

Title :  CRYSTAL STRUCTURE OF T4 POLYNUCLEOTIDE KINASE
 
Authors :  E. A. Galburt, J. Pelletier, G. Wilson, B. L. Stoddard
Date :  20 May 02  (Deposition) - 09 Oct 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Kinase, Phosphatase, Alpha/Beta, P-Loop, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. A. Galburt, J. Pelletier, G. Wilson, B. L. Stoddard
Structure Of A Trna Repair Enzyme And Molecular Biology Workhorse: T4 Polynucleotide Kinase.
Structure V. 10 1249 2002
PubMed-ID: 12220496  |  Reference-DOI: 10.1016/S0969-2126(02)00835-3

(-) Compounds

Molecule 1 - POLYNUCLEOTIDE KINASE
    ChainsA
    EC Number2.7.1.78
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificENTEROBACTERIA PHAGE T4
    Organism Taxid10665
    SynonymPNK, POLYNUCLEOTIDE 5'-HYDROXYL-KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 56)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2DMS4Ligand/IonDIMETHYL SULFOXIDE
3MSE48Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:11 , GLY A:12 , SER A:13 , GLY A:14 , LYS A:15 , SER A:16 , THR A:17 , ARG A:122 , ARG A:126BINDING SITE FOR RESIDUE ADP A 900
2AC2SOFTWAREGLU A:108 , HIS A:109 , ARG A:226 , HOH A:627BINDING SITE FOR RESIDUE DMS A 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LTQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LTQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LTQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LTQ)

(-) Exons   (0, 0)

(no "Exon" information available for 1LTQ)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:298
 aligned with KIPN_BPT4 | P06855 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:301
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
            KIPN_BPT4     1 MKKIILTIGCPGSGKSTWAREFIAKNPGFYNINRDDYRQSIMAHEERDEYKYTKKKEGIVTGMQFDTAKSILYGGDSVKGVIISDTNLNPERRLAWETFAKEYGWKVEHKVFDVPWTELVKRNSKRGTKAVPIDVLRSMYKSMREYLGLPVYNGTPGKPKAVIFDVDGTLAKMNGRGPYDLEKCDTDVINPMVVELSKMYALMGYQIVVVSGRESGTKEDPTKYYRMTRKWVEDIAGVPLVMQCQREQGDTRKDDVVKEEIFWKHIAPHFDVKLAIDDRTQVVEMWRRIGVECWQVASGDF 301
               SCOP domains d1ltqa2 A:1-152 Polynucleotide kinase, kinase do   main                                                                                                 d1ltqa1 A:153-301 Polynucleotide kinase, phosphatase domain                                                                                           SCOP domains
               CATH domains -1ltqA01 A:2-149 P-loop containing nucleotide tr   iphosphate hydrolases                                                                             ---------1ltqA02 A:159-301  [code=3.40.50.1000, no name defined]                                                                                         CATH domains
               Pfam domains ---AAA_33-1ltqA01 A:4-147                                                                                                                          ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhh..eeeehhhhhhhhhh......---.hhhhhhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...........eeeeee..............hhhhhhhh..hhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhhhh......eeee.......hhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhh...eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ltq A   1 mKKIILTIGCPGSGKSTWAREFIAKNPGFYNINRDDYRQSImAHEERD---YTKKKEGIVTGmQFDTAKSILYGGDSVKGVIISDTNLNPERRLAWETFAKEYGWKVEHKVFDVPWTELVKRNSKRGTKAVPIDVLRSmYKSmREYLGLPVYNGTPGKPKAVIFDVDGTLAKmNGRGPYDLEKCDTDVINPmVVELSKmYALmGYQIVVVSGRESGTKEDPTKYYRmTRKWVEDIAGVPLVmQCQREQGDTRKDDVVKEEIFWKHIAPHFDVKLAIDDRTQVVEmWRRIGVECWQVASGDF 301
                            |       10        20        30        40 |     | - |      60  |     70        80        90       100       110       120       130       140  |    150       160       170  |    180       190 |     200  |    210       220      |230       240 |     250       260       270       280    |  290       300 
                            |                                       42-MSE48  52         63-MSE                                                                     139-MSE                           173-MSE            192-MSE  |   |                     227-MSE        242-MSE                                    285-MSE            
                            1-MSE                                                                                                                                       143-MSE                                                 199-MSE                                                                                                  
                                                                                                                                                                                                                                    203-MSE                                                                                              

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (KIPN_BPT4 | P06855)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0046404    ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity    Catalysis of the reaction: ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA.
    GO:0047846    deoxynucleotide 3'-phosphatase activity    Catalysis of the reaction: a deoxynucleoside 3'-phosphate + H2O = a deoxynucleoside + phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KIPN_BPT4 | P068551ly1 1rc8 1rpz 1rrc 2ia5 5uj0

(-) Related Entries Specified in the PDB File

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