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(-) Description

Title :  STRUCTURE OF YEAST POLY(A) POLYMERASE WITH ATP AND OLIGO(A)
 
Authors :  A. Bohm, P. Balbo
Date :  04 Jun 07  (Deposition) - 28 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,X
Keywords :  Protein Rna Complex Atp Polymerase Complex, Transferase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. B. Balbo, A. Bohm
Mechanism Of Poly(A) Polymerase: Structure Of The Enzyme-Mgatp-Rna Ternary Complex And Kinetic Analysis.
Structure V. 15 1117 2007
PubMed-ID: 17850751  |  Reference-DOI: 10.1016/J.STR.2007.07.010
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(P*AP*AP*AP*AP*A)-3'
    Chains: X
    Engineered: YES
    Other Details: SYNTHETIC
    Synthetic: YES
 
Molecule 2 - POLY(A) POLYMERASE
    Chains: A
    EC Number: 2.7.7.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PAP1
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: PAP, POLYNUCLEOTIDE ADENYLYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AX

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric/Biological Unit (3, 19)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2EDO17Ligand/Ion1,2-ETHANEDIOL
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:100 , ASP A:102 , ATP A:605 , HOH A:1097BINDING SITE FOR RESIDUE MG A 602
02AC2SOFTWARETYR A:87 , GLY A:88 , SER A:89 , ASP A:100 , ASP A:102 , GLY A:190 , LYS A:215 , TYR A:224 , ASN A:226 , GLY A:233 , VAL A:234 , MET A:310 , ALA A:312 , MG A:602 , HOH A:727 , HOH A:817 , HOH A:872 , HOH A:880 , HOH A:896 , HOH A:919 , HOH A:920 , HOH A:966 , HOH A:1000 , HOH A:1088 , HOH A:1097 , A X:5BINDING SITE FOR RESIDUE ATP A 605
03AC3SOFTWARELYS A:53 , GLN A:56 , GLU A:57 , GLN A:60 , TYR A:247 , ARG A:258 , ILE A:262 , HOH A:827 , HOH A:1142BINDING SITE FOR RESIDUE EDO A 701
04AC4SOFTWAREVAL A:16 , ALA A:250 , ARG A:258 , HOH A:820 , HOH A:911 , HOH A:980BINDING SITE FOR RESIDUE EDO A 702
05AC5SOFTWARELYS A:34 , PHE A:39 , GLU A:418 , HOH A:733 , HOH A:755BINDING SITE FOR RESIDUE EDO A 703
06AC6SOFTWAREASN A:23 , ASN A:26 , ASP A:27 , CYS A:251 , HOH A:805BINDING SITE FOR RESIDUE EDO A 704
07AC7SOFTWARESER A:28 , SER A:344 , TRP A:345 , HOH A:921 , HOH A:1013BINDING SITE FOR RESIDUE EDO A 705
08AC8SOFTWAREPRO A:276 , ILE A:277 , HOH A:746 , HOH A:764BINDING SITE FOR RESIDUE EDO A 706
09AC9SOFTWAREGLU A:132 , ILE A:146 , LYS A:147 , HOH A:731 , HOH A:768BINDING SITE FOR RESIDUE EDO A 707
10BC1SOFTWAREGLN A:60 , TYR A:64 , ARG A:78 , GLY A:81BINDING SITE FOR RESIDUE EDO A 708
11BC2SOFTWAREA X:2BINDING SITE FOR RESIDUE EDO X 709
12BC3SOFTWARELYS A:351 , LYS A:407 , PHE A:409 , VAL A:521 , ASP A:523 , HOH A:960 , HOH A:1018BINDING SITE FOR RESIDUE EDO A 710
13BC4SOFTWAREARG A:221 , LYS A:351 , ASP A:353 , HOH A:1071BINDING SITE FOR RESIDUE EDO A 711
14BC5SOFTWAREGLU A:32 , GLU A:36 , ARG A:220 , ALA A:346 , PHE A:349 , GLU A:350BINDING SITE FOR RESIDUE EDO A 712
15BC6SOFTWAREVAL A:16 , GLY A:17 , ALA A:18 , ASP A:455BINDING SITE FOR RESIDUE EDO A 713
16BC7SOFTWAREVAL A:49 , LYS A:53 , GLU A:265 , ASN A:267 , HOH A:791 , HOH A:810 , HOH A:925BINDING SITE FOR RESIDUE EDO A 714
17BC8SOFTWAREALA A:139 , PHE A:140 , HOH A:1054 , A X:4BINDING SITE FOR RESIDUE EDO X 715
18BC9SOFTWAREPHE A:470 , LYS A:478 , VAL A:479 , A X:1BINDING SITE FOR RESIDUE EDO A 716
19CC1SOFTWARESER A:168 , VAL A:329 , HOH A:765 , HOH A:944BINDING SITE FOR RESIDUE EDO A 717

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q66)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Trp A:268 -Pro A:269
2Tyr A:307 -Pro A:308
3Asn A:438 -Ala A:439
4Phe A:495 -Asn A:496

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q66)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q66)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YKR002W1YKR002W.1XI:442875-4445811707PAP_YEAST1-5685681A:5-529 (gaps)525

(-) 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:519
 aligned with PAP_YEAST | P29468 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:525
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524     
            PAP_YEAST     5 KVFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYEVSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLRERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGSDEQHLKWSGLVESKVRLLVMKLEVLAGIKIAHPFTKPFESSYCCPTEDDYEMIQDKYGSHKTETALNALKLVTDENKEEESIKDAPKAYLSTMYIGLDFNIENKKEKVDIHIPCTEFVNLCRSFNEDYGDHKVFNLALRFVKGYDLPDEVFDENEKRP 529
               SCOP domains d2q66a2 A:5-201 Poly(A) polymerase, PAP, N-terminal domain                                                                                                                                           d2q66a1 A:202-351 Poly(A) polymerase, PAP, middle domain                                                                                              d2q66a3 A:352-529 Poly(A) polymerase, PAP, C-terminal domain                                                                                                                       SCOP domains
               CATH domains 2q66A01 A:5-39,A:196-352           2q66A02 A:40-195 Beta Polymerase, domain 2                                                                                                                  2q66A01 A:5-39,A:196-352  [code=1.10.1410.10, no name defined]                                                                                               2q66A03 A:353-521  [code=3.30.70.590, no name defined]                                                                                                                   -------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------NTP_transf_2-2q66A01 A:72-161                                                             -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PAP_RNA-bind-2q66A02 A:353-529                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) PAP_central-2q66A03 A:5-352                                                                                                                                                                                                                                                                                                                                 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..eeeeehhhhhh.......eeeeeee....hhhhhhhhhhhhhhh...eeeeeee......eeeeee..eeeeeeeee.............hhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....ee..................hhhhhh....ee.............hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhh.eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee....eeeeee..hhhhhhhhhhhh....hhhhhh.........-.hhhhhhh.eeeeeeeeeeeee..-----...hhhhhhhhhhhhhh..........eeeeeeeee.hhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-529 (gaps) UniProt: 1-568 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 2q66 A   5 KVFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYEVSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLRERKELDEIAPVPDAFVPIIKIKFSGISIALICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGSDEQHLKWSGLVESKVRLLVMKLEVLAGIKIAHPFTKPFESSYCCPTEDDYEMIQDKYGSHKTETALNALKLVTDEN-EEESIKDAPKAYLSTMYIGLDFNI-----KVDIHIPCTEFVNLCRSFNEDYGDHKVFNLALRFVKGYDLPDEVFDENEKRP 529
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444  | |  454       464       | -   |   484       494       504       514       524     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    447 |                    472   478                                                   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      449                                                                                


Chain X from PDB  Type:RNA  Length:5
                                     
                 2q66 X   1 AAAAA   5
   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
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: NTP_transf (45)
(-)
Clan: no clan defined [family: PAP_RNA-bind] (3)
(-)
Clan: no clan defined [family: PAP_central] (3)

(-) 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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  2q66
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  PAP_YEAST | P29468
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 Related Entries

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

UniProtKB/Swiss-Prot
        PAP_YEAST | P29468: 1fa0 2hhp 2o1p 3c66

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Q66)