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(-) Description

Title :  DC26 MUTANT OF VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE AND M7G(5')PPPG
 
Authors :  A. E. Hodel, P. D. Gershon, F. A. Quiocho
Date :  16 Dec 96  (Deposition) - 17 Sep 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Methyltransferase, Rna Cap, Poly(A) Polymerase, Vaccinia, Mrna Processing, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. E. Hodel, P. D. Gershon, X. Shi, S. M. Wang, F. A. Quiocho
Specific Protein Recognition Of An Mrna Cap Through Its Alkylated Base.
Nat. Struct. Biol. V. 4 350 1997
PubMed-ID: 9145102  |  Reference-DOI: 10.1038/NSB0597-350
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VP39
    Cell LineBL21
    ChainsA
    EC Number2.7.7.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidBL21
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    MutationYES
    Organism ScientificVACCINIA VIRUS
    Organism Taxid10254
    StrainWR
    SynonymPOLY(A) POLYMERASE REGULATORY SUBUNIT

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1M7G1Ligand/Ion7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1M7G2Ligand/Ion7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:39 , LEU A:42 , TYR A:66 , GLY A:68 , SER A:69 , ALA A:70 , PRO A:71 , GLY A:72 , HIS A:74 , ASP A:95 , ARG A:97 , ARG A:114 , PHE A:115 , VAL A:116 , ASP A:138 , VAL A:139 , ARG A:140BINDING SITE FOR RESIDUE SAH A 400
2AC2SOFTWARETYR A:22 , ALA A:27 , PRO A:148 , ARG A:177 , PHE A:180 , ASP A:182 , TYR A:204 , GLU A:233 , HOH A:592 , HOH A:603 , HOH A:624BINDING SITE FOR RESIDUE M7G A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VP3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric 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 2VP3)

(-) PROSITE Motifs  (1, 1)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VP3)

(-) 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:291
 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 d2vp3a_ A: Polymerase regulatory subunit VP39                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2vp3A00 A:1-297 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhh........hhhhh........hhhhhhhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhh.....eeeeee.....hhh.....eeeee....hhhhhhhhhhh....eeeee....------..hhhhhhhhhhhhhhhhhh...eeeeee....hhh....eeee..eee...........eeeeee.......eeee.hhhhhhhhhhhhhhhh.hhh............hhhhhhhhhhhh.........hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SAM_MT_2O_PK  PDB: A:4-262 UniProt: 4-262                                                                                                                                                                                                                          ----------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vp3 A   1 MDVVSLDKPFMYFEEIDNELDYEPESANEVAKKLPYQGQLKLLLGELFFLSKLQRHGILDGATVVYIGSAPGTHIRYLRDHFYNLGVIIKWMLIDGRHHDPILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVRS------PSTADLLSNYALQNVMISILNPVASSLKWRCPFPDQWIKDFYIPHGNKMLQPFAPSYSAEMRLLSIYTGENMRLTRVTKSDAVNYEKKMYYLNKIVRNKVVVNFDYPNQEYDYFHMYFMLRTVYCNKTFPTTKAKVLFLQQSIFRFLNIP 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       
                                                                                                                                                                      141    148                                                                                                                                                     

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2VP3)

(-) Gene Ontology  (14, 14)

Asymmetric 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.

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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 2ga9 2gaf 3er8 3er9 3erc 3mag 3mct 4dcg

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2VP3)