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(-) Description

Title :  STRUCTURE OF YEAST POLY(A) POLYMERASE IN A CLOSED CONFORMATION.
 
Authors :  A. Bohm, J. Toth
Date :  28 Jun 06  (Deposition) - 23 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Template-Independent Rna Polymerase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. B. Balbo, J. Toth, A. Bohm
X-Ray Crystallographic And Steady State Fluorescence Characterization Of The Protein Dynamics Of Yeast Polyadenylate Polymerase.
J. Mol. Biol. V. 366 1401 2007
PubMed-ID: 17223131  |  Reference-DOI: 10.1016/J.JMB.2006.12.030

(-) Compounds

Molecule 1 - POLY(A) POLYMERASE
    ChainsA
    EC Number2.7.7.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GenePAP1
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymPAP, POLYNUCLEOTIDE ADENYLYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1FLC2Ligand/IonCITRATE ANION
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:20 , ASN A:23 , LYS A:24 , THR A:417 , GLU A:418 , ASP A:419BINDING SITE FOR RESIDUE FLC A 531
2AC2SOFTWARETYR A:224 , GLY A:232 , GLY A:233 , VAL A:234 , MG A:533 , HOH A:582 , HOH A:670 , HOH A:759 , HOH A:761 , HOH A:817 , HOH A:833 , HOH A:866BINDING SITE FOR RESIDUE FLC A 532
3AC3SOFTWAREASP A:102 , ASP A:154 , FLC A:532BINDING SITE FOR RESIDUE MG A 533

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HHP)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Trp A:268 -Pro A:269
2Tyr A:307 -Pro A:308
3Asn A:438 -Ala A:439
4Ala A:439 -Leu A:440
5Leu A:440 -Lys A:441
6Lys A:478 -Val A:479
7Tyr A:499 -Gly A:500

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HHP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HHP)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YKR002W1YKR002W.1XI:442875-4445811707PAP_YEAST1-5685681A:4-530 (gaps)527

(-) 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:508
 aligned with PAP_YEAST | P29468 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:527
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       
            PAP_YEAST     4 QKVFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYEVSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLRERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGSDEQHLKWSGLVESKVRLLVMKLEVLAGIKIAHPFTKPFESSYCCPTEDDYEMIQDKYGSHKTETALNALKLVTDENKEEESIKDAPKAYLSTMYIGLDFNIENKKEKVDIHIPCTEFVNLCRSFNEDYGDHKVFNLALRFVKGYDLPDEVFDENEKRPS 530
               SCOP domains d2hhpa2 A:4-201 Poly(A) polymerase, PAP, N-terminal domain                                                                                                                                            d2hhpa1 A:202-351 Poly(A) polymerase, PAP, middle domain                                                                                              d2hhpa3 A:352-530 Poly(A) polymerase, PAP, C-terminal domain                                                                                                                        SCOP domains
               CATH domains 2hhpA01 A:4-39,A:196-352            2hhpA02 A:40-195 Beta Polymerase, domain 2                                                                                                                  2hhpA01 A:4-39,A:196-352  [code=1.10.1410.10, no name defined]                                                                                               2hhpA03 A:353-522  [code=3.30.70.590, no name defined]                                                                                                                    -------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..eeeeehhhhhh.......eeeeeee....hhhhhhhhhhhhhhh...eeeeeee......eeeeee..eeeeeeeee.............hhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....ee..................hhhhhh....ee.............hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhh..eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee....eeeeee....hhhhhhhhhh.hhhhhh......---------------.eeeeeeeeeeeee.----.....hhhhhhhhhhhhhhh.........eeeeeeeehhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:4-530 (gaps) UniProt: 1-568 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Transcript 1
                 2hhp A   4 QKVFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYEVSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLRERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGSDEQHLKWSGLVESKVRLLVMKLEVLAGIKIAHPFTKPFESSYCCPTEDDYEMIQDKYGSHKTETALNALK---------------PKAYLSTMYIGLDFN----KEKVDIHIPCTEFVNLCRSFNEDYGDHKVFNLALRFVKGYDLPDEVFDENEKRPS 530
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       | -         -   |   463       | -  |    483       493       503       513       523       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               441             457           471  476                                                      

   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  (0, 0)

(no "Pfam Domain" information available for 2HHP)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PAP_YEAST | P29468)
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: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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0071050    snoRNA polyadenylation    The enzymatic addition of a sequence of adenylyl residues at the 3' end of snoRNA molecule. In eukaryotes, this occurs in conjunction with termination of transcription of precursor snoRNA molecules and may occur post-transcriptionally on incorrectly processed molecules targeted for degradation.
cellular component
    GO:0005847    mRNA cleavage and polyadenylation specificity factor complex    A multisubunit complex that binds to the canonical AAUAAA hexamer and to U-rich upstream sequence elements on the pre-mRNA, thereby stimulating the otherwise weakly active and nonspecific polymerase to elongate efficiently RNAs containing a poly(A) signal.
    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
        PAP_YEAST | P294681fa0 2o1p 2q66 3c66

(-) Related Entries Specified in the PDB File

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