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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HETERODIMERIC VACCINIA VIRUS POLYADENYLATE POLYMERASE WITH BOUND ATP-GAMMA-S
 
Authors :  C. M. Moure, B. R. Bowman, P. D. Gershon, F. A. Quiocho
Date :  08 Mar 06  (Deposition) - 16 May 06  (Release) - 15 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Polyadenylate Polymerase, Nucleotidyltransferase, Poxvirus, Heterodimer, Processivity, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. M. Moure, B. R. Bowman, P. D. Gershon, F. A. Quiocho
Crystal Structures Of The Vaccinia Virus Polyadenylate Polymerase Heterodimer: Insights Into Atp Selectivity And Processivity.
Mol. Cell V. 22 339 2006
PubMed-ID: 16678106  |  Reference-DOI: 10.1016/J.MOLCEL.2006.03.015

(-) Compounds

Molecule 1 - CAP-SPECIFIC MRNA (NUCLEOSIDE-2'-O-)-METHYLTRANSFERASE
    ChainsA
    EC Number2.1.1.57
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21 DE3
    Expression System Taxid469008
    Expression System VectorPLASMID
    Expression System Vector TypePPG177
    MutationYES
    Organism ScientificVACCINIA VIRUS
    Organism Taxid10245
    SynonymPOLYA, POLYMERASE REGULATORY SUBUNIT, POLYA, POLYMERASE SMALL SUBUNIT, PAP-S, VP39
 
Molecule 2 - POLY(A) POLYMERASE CATALYTIC SUBUNIT
    ChainsD
    EC Number2.7.7.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21 ROSETTA
    Expression System Taxid562
    MutationYES
    Organism ScientificVACCINIA VIRUS
    Organism Taxid10245
    SynonymPOLYA, POLYMERASE LARGE SUBUNIT, PAP-L, VP55

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1AGS2Ligand/IonPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
2CA2Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP D:202 , ASP D:204 , AGS D:482 , HOH D:494BINDING SITE FOR RESIDUE CA D 480
2AC2SOFTWAREASP D:202 , ASP D:204 , HOH D:621BINDING SITE FOR RESIDUE CA D 481
3AC3SOFTWARETYR D:186 , GLY D:187 , SER D:188 , ASP D:204 , GLN D:281 , ASN D:284 , MET D:285 , MET D:288 , ARG D:294 , LYS D:304 , ASN D:402 , CA D:480 , HOH D:492 , HOH D:551 , HOH D:575 , HOH D:607BINDING SITE FOR RESIDUE AGS D 482
4AC4SOFTWAREPHE D:47 , ASN D:48 , ILE D:51 , PHE D:52 , LEU D:55 , THR D:109 , GLY D:113 , THR D:116BINDING SITE FOR RESIDUE AGS D 483

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GA9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:70 -Pro A:71
2His A:129 -Pro A:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GA9)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_2O_PKPS51612 Poxvirus/kinetoplastid-type ribose 2'-O-methyltransferase (EC 2.1.1.57) family profile.MCE_VACCW4-262  1A:4-262

(-) Exons   (0, 0)

(no "Exon" information available for 2GA9)

(-) 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:288
 aligned with MCE_VACCW | P07617 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:297
                                    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       
            MCE_VACCW     1 MDVVSLDKPFMYFEEIDNELDYEPESANEVAKKLPYQGQLKLLLGELFFLSKLQRHGILDGATVVYIGSAPGTHIRYLRDHFYNLGVIIKWMLIDGRHHDPILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVRSKRGGNEPSTADLLSNYALQNVMISILNPVASSLKWRCPFPDQWIKDFYIPHGNKMLQPFAPSYSAEMRLLSIYTGENMRLTRVTKSDAVNYEKKMYYLNKIVRNKVVVNFDYPNQEYDYFHMYFMLRTVYCNKTFPTTKAKVLFLQQSIFRFLNIP 297
               SCOP domains d2ga9a_ A: automated match      es                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2ga9A00 A:1-297 Vaccinia V      irus protein VP39                                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.......hhhhh..........------...hhhhhhhhhhhhhhhhhhhhh......eeeee......hhhhhhhhhhhh....eeeeee....hhhhh....eeeee...hhhhhhhhhhhhh...eeeee....---....hhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhh...eeee..eee...........eeeeee.......eeeehhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SAM_MT_2O_PK  PDB: A:4-262 UniProt: 4-262                                                                                                                                                                                                                          ----------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ga9 A   1 MDVVSLDKPFMYFEEIDNELDYEPES------KLPYQGQLKLLLGELFFLSKLQRHGILDGATVVYIGSAPGTHIRYLRDHFYNLGVIIKWMLIDGRHHDPILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVAS---GNEPSTADLLSNYALQNVMISILNPVASSLKWRCPFPDQWIKDFYIPHGNKMLQPFAPSYSAEMRLLSIYTGENMRLTRVTKSDAVNYEKKMYYLNKIVRNKVVVNFDYPNQEYDYFHMYFMLRTVYCNKTFPTTKAKVLFLQQSIFRFLNIP 297
                                    10        20     |   -  |     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       
                                                    26     33                                                                                                         141 145                                                                                                                                                        

Chain D from PDB  Type:PROTEIN  Length:445
 aligned with PAP1_VACCW | P23371 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:468
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471        
           PAP1_VACCW    12 NITLKIIETYLGRVPSVNEYHMLKLQARNIQKITVFNKDIFVSLVKKNKKRFFSDVNTSASEIKDRILSYFSKQTQTYNIGKLFTIIELQSVLVTTYTDILGVLTIKAPNVISSKISYNVTSMEELARDMLNSMNVAVIDKAKVMGRHNVSSLVKNVNKLMEEYLRRHNKSCICYGSYSLYLINPNIRYGDIDILQTNSRTFLIDLAFLIKFITGNNIILSKIPYLRNYMVIKDENDNHIIDSFNIRQDTMNVVPKIFIDNIYIVDPTFQLLNMIKMFSQIDRLEDLSKDPEKFNARMATMLEYVRYTHGIVFDGKRNNMPMKCIIDENNRIVTVTTKDYFSFKKCLVYLDENVLSSDILDLNADTSCDFESVTNSVYLIHDNIMYTYFSNTILLSDKGKVHEISARGLCAHILLYQMLTSGEYKQCLSDLLNSMMNRDKIPIYSHTERDKKPGRHGFINIEKDIIVF 479
               SCOP domains d2ga9d1 D:12-479 Poly(A) polymerase catalytic subunit, PAPL                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh------------hhhhhhhhhhhhhhhhh...-----------..hhhhhhhhhhhhhhhhh...eeeehhhhhhh..........eeee.hhhhhhhhhhhhhhhhhh...eeee......eeeee.....eeeeeee.hhhhhhhh.eeee..eeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeee....eeeee........eeeee.hhhhhhhhhhhh.....ee.hhhh..eeeee..eeeee.....eeee..eehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..........ee..........eeee....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ga9 D  12 NITLKIIETYLGRVPSVNEYHMLKSQARNIQKITVFNKDIFVSLVKKNKKRFFSDVNTSASEIKDRILSYFSKQTQTYNIGKLFTIIELQSVLVTTYTDILGVLTI------------NVTSMEELARDMLNSMNVAV-----------VSSLVKNVNKLMEEYLRRHNKSCICYGSYSLYLINPNIRYGDIDILQTNSRTFLIDLAFLIKFITGNNIILSKIPYLRNYMVIKDENDNHIIDSFNIRQDTMNVVPKIFIDNIYIVDPTFQLLNMIKMFSQIDRLEDLSKDPEKFNARMATMLEYVRYTHGIVFDGKRNNMPMKCIIDENNRIVTVTTKDYFSFKKCLVYLDENVLSSDILDLNADTSCDFESVTNSVYLIHDNIMYTYFSNTILLSDKGKVHEISARGLCAHILLYQMLTSGEYKQCLSDLLNSMMNRDKIPIYSHTERDKKPGRHGFINIEKDIIVF 479
                                    21        31        41        51        61        71        81        91       101       111     |   -       131       141       | -       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471        
                                                                                                                                   117          130                149         161                                                                                                                                                                                                                                                                                                                              

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GA9)

(-) Gene Ontology  (17, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MCE_VACCW | P07617)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004483    mRNA (nucleoside-2'-O-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + m7G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppRm-RNA. R may be guanosine or adenosine.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
    GO:0006370    7-methylguanosine mRNA capping    Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
    GO:0080009    mRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an mRNA molecule.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    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.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
cellular component
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

Chain D   (PAP1_VACCW | P23371)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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: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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MCE_VACCW | P076171av6 1b42 1bky 1eam 1eqa 1jsz 1jte 1jtf 1p39 1v39 1vp3 1vp9 1vpt 2gaf 2vp3 3er8 3er9 3erc 3mag 3mct 4dcg
        PAP1_VACCW | P233712gaf 3er8 3er9 3erc 3owg

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2GA9)