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(-) Description

Title :  HUMAN POLY(ADP-RIBOSE) POLYMERASE 14 (PARP14/ARTD8) - CATALYTIC DOMAIN IN COMPLEX WITH A PYRIMIDINE-LIKE INHIBITOR
 
Authors :  T. Karlberg, M. Moche, C. H. Arrowsmith, H. Berglund, C. Bountra, A. M. E T. Ekblad, S. Graslund, E. Kouznetsova, P. Nordlund, T. Nyman, A. G. Th L. Tresaugues, J. Weigelt, H. Schuler, Structural Genomics Consor (Sgc)
Date :  28 Jun 11  (Deposition) - 20 Jul 11  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Diphtheria Toxin Like Fold, Transferase, Nad+, Adp-Ribosylation, Transferase-Transferase Inhibitor Complex, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Wahlberg, T. Karlberg, E. Kouznetsova, N. Markova, A. Macchiarulo A. G. Thorsell, E. Pol, A. Frostell, T. Ekblad, D. Oncu, B. Kull, G. M. Robertson, R. Pellicciari, H. Schuler, J. Weigelt
Family-Wide Chemical Profiling And Structural Analysis Of Parp And Tankyrase Inhibitors.
Nat. Biotechnol. V. 30 283 2012
PubMed-ID: 22343925  |  Reference-DOI: 10.1038/NBT.2121

(-) Compounds

Molecule 1 - POLY [ADP-RIBOSE] POLYMERASE 14
    ChainsA, B
    EC Number2.4.2.30
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-BSA4
    Expression System StrainBL21(DE3) R3 PRARE
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN
    GeneBAL2, KIAA1268, PARP14
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPARP-14, B AGGRESSIVE LYMPHOMA PROTEIN 2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1FDR2Ligand/Ion2-METHYL-3,5,6,7-TETRAHYDRO-4H-CYCLOPENTA[4,5]THIENO[2,3-D]PYRIMIDIN-4-ONE
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1FDR1Ligand/Ion2-METHYL-3,5,6,7-TETRAHYDRO-4H-CYCLOPENTA[4,5]THIENO[2,3-D]PYRIMIDIN-4-ONE
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FDR1Ligand/Ion2-METHYL-3,5,6,7-TETRAHYDRO-4H-CYCLOPENTA[4,5]THIENO[2,3-D]PYRIMIDIN-4-ONE
2GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1FDR2Ligand/Ion2-METHYL-3,5,6,7-TETRAHYDRO-4H-CYCLOPENTA[4,5]THIENO[2,3-D]PYRIMIDIN-4-ONE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:289 , HIS A:1601 , GLY A:1602 , TYR A:1633 , ALA A:1635 , TYR A:1640 , SER A:1641 , TYR A:1646 , PRO A:1682 , GLN A:1683BINDING SITE FOR RESIDUE FDR A 1
2AC2SOFTWAREHOH A:2 , HOH A:65 , HOH A:264 , HIS A:1601 , THR A:1603 , ARG A:1618BINDING SITE FOR RESIDUE GOL A 1721
3AC3SOFTWAREHOH B:88 , HIS B:1601 , GLY B:1602 , GLY B:1622 , TYR B:1633 , SER B:1641 , TYR B:1646BINDING SITE FOR RESIDUE FDR B 2

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:1537 -B:1537

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SMJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SMJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SMJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3SMJ)

(-) 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:188
 aligned with PAR14_HUMAN | Q460N5 from UniProtKB/Swiss-Prot  Length:1801

    Alignment length:188
                                  1623      1633      1643      1653      1663      1673      1683      1693      1703      1713      1723      1733      1743      1753      1763      1773      1783      1793        
         PAR14_HUMAN   1614 QQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK 1801
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhhh......hhhhh.....eeee.hhhhhh............eeeeeeeee...eee.....................eee.......eeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3smj A 1533 QQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK 1720
                                  1542      1552      1562      1572      1582      1592      1602      1612      1622      1632      1642      1652      1662      1672      1682      1692      1702      1712        

Chain B from PDB  Type:PROTEIN  Length:186
 aligned with PAR14_HUMAN | Q460N5 from UniProtKB/Swiss-Prot  Length:1801

    Alignment length:186
                                  1625      1635      1645      1655      1665      1675      1685      1695      1705      1715      1725      1735      1745      1755      1765      1775      1785      1795      
         PAR14_HUMAN   1616 NFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK 1801
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhhhh..eeeeeeeeehhhhhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhhh................eeee.hhhhhh............eeeeeeeee...eee.....................eee.......eeee.hhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3smj B 1535 NFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK 1720
                                  1544      1554      1564      1574      1584      1594      1604      1614      1624      1634      1644      1654      1664      1674      1684      1694      1704      1714      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3SMJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SMJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SMJ)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PAR14_HUMAN | Q460N5)
molecular function
    GO:0003950    NAD+ ADP-ribosyltransferase activity    Catalysis of the reaction: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor.
    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.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PAR14_HUMAN | Q460N53goy 3q6z 3q71 3se2 3smi 3vfq 4abk 4abl 4d86 4f1l 4f1q 4py4 5lxp 5lyh 5nqe 5v7t 5v7w

(-) Related Entries Specified in the PDB File

3goy SAME PROTEIN COMPLEXED WITH 3AB
3se2 SAME PROTEIN COMPLEXED WITH 6(5H)-PHENANTHRIDINONE
3smi SAME PROTEIN COMPLEXED WITH A QUINAZOLINE INHIBITOR