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(-) Description

Title :  CRYSTAL STRUCTURE OF POLY(A) POLYMERASE IN COMPLEX WITH 3'-DATP AND MAGNESIUM CHLORIDE
 
Authors :  G. Martin, A. Moglich, W. Keller, S. Doublie
Date :  16 Aug 03  (Deposition) - 07 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Mrna Processing, Nucleotidyl Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Martin, A. Moglich, W. Keller, S. Doublie
Biochemical And Structural Insights Into Substrate Binding And Catalytic Mechanism Of Mammalian Poly(A) Polymerase.
J. Mol. Biol. V. 341 911 2004
PubMed-ID: 15328606  |  Reference-DOI: 10.1016/J.JMB.2004.06.047
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLY(A) POLYMERASE ALPHA
    ChainsA
    EC Number2.7.7.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGM10 BOVPAP513
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-513
    GenePAPOLA OR PAP
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    SynonymPAP, POLYNUCLEOTIDE ADENYLYLTRANSFERASE ALPHA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
13AT1Ligand/Ion3'-DEOXYADENOSINE-5'-TRIPHOSPHATE
2CSD2Mod. Amino Acid3-SULFINOALANINE
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:113 , ASP A:115 , 3AT A:1000BINDING SITE FOR RESIDUE MG A 1002
2AC2SOFTWAREPHE A:100 , GLY A:101 , SER A:102 , ASP A:115 , ASN A:202 , VAL A:206 , LYS A:228 , TYR A:237 , GLY A:246 , VAL A:247 , THR A:317 , MG A:1002 , HOH A:2043 , HOH A:2050 , HOH A:2060 , HOH A:2069 , HOH A:2108 , HOH A:2117BINDING SITE FOR RESIDUE 3AT A 1000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q78)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:281 -Pro A:282
2Tyr A:320 -Pro A:321

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q78)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q78)

(-) Exons   (15, 15)

Asymmetric/Biological Unit (15, 15)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENSBTAT000000053001bENSBTAE00000429997chr21:61558615-6155866854PAPOA_BOVIN1-330--
1.2ENSBTAT000000053002ENSBTAE00000392174chr21:61572974-61573147174PAPOA_BOVIN3-61591A:19-6143
1.3ENSBTAT000000053003ENSBTAE00000042583chr21:61573550-6157361667PAPOA_BOVIN61-83231A:61-8323
1.4ENSBTAT000000053004ENSBTAE00000042584chr21:61576385-6157646682PAPOA_BOVIN84-111281A:84-11128
1.5ENSBTAT000000053005ENSBTAE00000042586chr21:61578210-61578319110PAPOA_BOVIN111-147371A:111-14737
1.6ENSBTAT000000053006ENSBTAE00000042587chr21:61578770-6157882354PAPOA_BOVIN148-165181A:148-16518
1.7ENSBTAT000000053007ENSBTAE00000042589chr21:61581599-61581710112PAPOA_BOVIN166-203381A:166-20338
1.8ENSBTAT000000053008ENSBTAE00000042592chr21:61582361-6158245090PAPOA_BOVIN203-233311A:203-23331
1.9ENSBTAT000000053009ENSBTAE00000042594chr21:61582541-61582679139PAPOA_BOVIN233-279471A:233-27947
1.10ENSBTAT0000000530010ENSBTAE00000381557chr21:61584527-6158459973PAPOA_BOVIN279-303251A:279-30325
1.11ENSBTAT0000000530011ENSBTAE00000042601chr21:61585936-61586056121PAPOA_BOVIN304-344411A:304-34441
1.12ENSBTAT0000000530012ENSBTAE00000042603chr21:61587008-6158709285PAPOA_BOVIN344-372291A:344-37229
1.13ENSBTAT0000000530013ENSBTAE00000042606chr21:61591631-6159168454PAPOA_BOVIN372-390191A:372-39019
1.14ENSBTAT0000000530014ENSBTAE00000042609chr21:61592212-61592331120PAPOA_BOVIN390-430411A:390-43041
1.15ENSBTAT0000000530015ENSBTAE00000042612chr21:61593451-61593560110PAPOA_BOVIN430-467381A:430-467 (gaps)38
1.16ENSBTAT0000000530016ENSBTAE00000042616chr21:61595973-61596094122PAPOA_BOVIN467-507411A:467-49832
1.17ENSBTAT0000000530017ENSBTAE00000042620chr21:61599064-61599206143PAPOA_BOVIN508-555480--
1.18ENSBTAT0000000530018ENSBTAE00000246874chr21:61601533-61601633101PAPOA_BOVIN555-589350--
1.19ENSBTAT0000000530019ENSBTAE00000042630chr21:61601831-61602051221PAPOA_BOVIN589-662740--
1.20ENSBTAT0000000530020ENSBTAE00000042634chr21:61605738-6160580063PAPOA_BOVIN663-683210--
1.21ENSBTAT0000000530021ENSBTAE00000042636chr21:61607657-6160773175PAPOA_BOVIN684-708250--
1.22aENSBTAT0000000530022aENSBTAE00000378893chr21:61609752-61610065314PAPOA_BOVIN709-739310--

(-) Sequences/Alignments

Asymmetric/Biological 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:470
 aligned with PAPOA_BOVIN | P25500 from UniProtKB/Swiss-Prot  Length:739

    Alignment length:480
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498
          PAPOA_BOVIN    19 HYGITSPISLAAPKETDCLLTQKLVETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRKQLHQLLP 498
               SCOP domains d1q78a2 A:19-214 Poly(A) polymerase, PAP, N-terminal domain                                                                                                                                         d1q78a1 A:215-364 Poly(A) polymerase, PAP, middle domain                                                                                              d1q78a3 A:365-498 Poly(A) polymerase, PAP, C-terminal domain                                                                           SCOP domains
               CATH domains -1q78A03 A:20-52,A:209-365        1q78A02 A:53-208 Beta Polymerase, domain 2                                                                                                                  1q78A03 A:20-52,A:209-365  [code=1.10.1410.10, no name defined]                                                                                              1q78A01 A:366-488  [code=3.30.70.590, no name defined]                                                                     ---------- CATH domains
           Pfam domains (1) --------------------------------------------------------NTP_transf_2-1q78A01 A:75-175                                                                        ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PAP_RNA-bind-1q78A02 A:366-498                                                                                                        Pfam domains (1)
           Pfam domains (2) PAP_central-1q78A03 A:19-365                                                                                                                                                                                                                                                                                                                               ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh....eeeeehhhhhh.......eeeeeee....hhhhhhhhhhhhhhh...eeeeeee......eeeeee..eeeeeeeee.............hhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...........................hhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhh..eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....ee..........eeeeeeeeeee.----------.hhhhhhhhhhhhhhhhhhh.......eeeeeeeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:19-61 UniProt: 3-61       ----------------------Exon 1.4  PDB: A:84-111     ------------------------------------Exon 1.6          Exon 1.7  PDB: A:166-203              ---------------------------------------------------------------------------Exon 1.10  PDB: A:279-303Exon 1.11  PDB: A:304-344                ---------------------------Exon 1.13          ---------------------------------------Exon 1.15  PDB: A:430-467 (gaps)      ------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.3  PDB: A:61-83 ---------------------------Exon 1.5  PDB: A:111-147             -------------------------------------------------------Exon 1.8  PDB: A:203-233       --------------------------------------------------------------------------------------------------------------Exon 1.12  PDB: A:344-372    -----------------Exon 1.14  PDB: A:390-430                ------------------------------------Exon 1.16  PDB: A:467-498        Transcript 1 (2)
           Transcript 1 (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:233-279 UniProt: 233-279      --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 1q78 A  19 HYGITSPISLAAPKETDcLLTQKLVETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRcIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKENPDKEEFRTMWVIGLVFK----------DLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRKQLHQLLP 498
                                    28       |38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438     |   -      |458       468       478       488       498
                                            36-CSD                                                                                                                                                          197-CSD                                                                                                                                                                                                                                                444        455                                           

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PAPOA_BOVIN | P25500)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0004652    polynucleotide adenylyltransferase activity    Catalysis of the template-independent extension of the 3'- end of an RNA or DNA strand by addition of one adenosine molecule at a time. Cannot initiate a chain 'de novo'. The primer, depending on the source of the enzyme, may be an RNA or DNA fragment, or oligo(A) bearing a 3'-OH terminal group.
    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:0031123    RNA 3'-end processing    Any process involved in forming the mature 3' end of an RNA molecule.
    GO:0043631    RNA polyadenylation    The enzymatic addition of a sequence of adenylyl residues at the 3' end of an RNA molecule.
    GO:0006378    mRNA polyadenylation    The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0031440    regulation of mRNA 3'-end processing    Any process that modulates the frequency, rate or extent of mRNA 3'-end processing, any process involved in forming the mature 3' end of an mRNA molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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
        PAPOA_BOVIN | P255001f5a 1q79

(-) Related Entries Specified in the PDB File

1q79 CRYSTAL STRUCTURE OF MAMMALIAN POLY(A) POLYMERASE