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(-) Description

Title :  CRYSTAL STRUCTURE OF INFECTIOUS BURSAL DISEASE VIRUS VP1 POLYMERASE, COCRYSTALLIZED WITH AN OLIGOPEPTIDE MIMICKING THE VP3 C-TERMINUS.
 
Authors :  D. Garriga, A. Navarro, J. Querol-Audi, F. Abaitua, J. F. Rodriguez, N. Verdaguer
Date :  07 Sep 07  (Deposition) - 27 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Ibdv, Infectious Bursal Disease Virus, Birnavirus, Polymerase, Vp1, Vp3, Activation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Garriga, A. Navarro, J. Querol-Audi, F. Abaitua, J. F. Rodriguez, N. Verdaguer
Activation Mechanism Of A Noncanonical Rna-Dependent Rna Polymerase.
Proc. Natl. Acad. Sci. Usa V. 104 20540 2007
PubMed-ID: 18077388  |  Reference-DOI: 10.1073/PNAS.0704447104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INFECTIOUS BURSAL VIRUS VP1 POLYMERASE
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell: HIGHFIVE CELLS
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: VP1 POLYMERASE (SEGMENT B)
    Organism Common: GUMBORO VIRUS
    Organism Scientific: INFECTIOUS BURSAL DISEASE VIRUS
    Organism Taxid: 10995
    Strain: SOROA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2R70)

(-) Sites  (0, 0)

(no "Site" information available for 2R70)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R70)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Arg A:115 -Pro A:116
2Leu A:260 -Pro A:261
3Thr A:295 -Lys A:296
4Glu A:394 -Pro A:395
5Lys A:761 -Pro A:762

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R70)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RDRP_DSRNA_BIRPS50524 RdRp of Birnaviridae dsRNA viruses catalytic domain profile.RDRP_IBDV398-598  1A:398-598

(-) Exons   (0, 0)

(no "Exon" information available for 2R70)

(-) 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:752
 aligned with RDRP_IBDV | Q9Q6Q5 from UniProtKB/Swiss-Prot  Length:881

    Alignment length:778
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796        
            RDRP_IBDV    27 DVEELLIPKVWVPPEDPLASPSRLAKFLRENGYKVLQPRSLPENEEYETDQILPDLAWMRQIEGAVLKPTLSLPIGDQEYFPKYYPTHRPSKEKPNAYPPDIALLKQMIYLFLQVPEANEGLKDEVTLLTQNIRDKAYGSGTYMGQATRLVAMKEVATGRNPNKDPLKLGYTFESIAQLLDITLPVGPPGEDDKPWVPLTRVPSRMLVLTGDVDGDFEVEDYLPKINLKSSSGLPYVGRTKGETIGEMIAISNQFLRELSTLLKQGAGTKGSNKKKLLSMLSDYWYLSCGLLFPKAERYDKSTWLTKTRNIWSAPSPTHLMISMITWPVMSNSPNNVLNIEGCPSLYKFNPFRGGLNRIVEWILAPEEPKALVYADNIYIVHSNTWYSIDLEKGEANCTRQHMQAAMYYILTRGWSDNGDPMFNQTWATFAMNIAPALVVDSSCLIMNLQIKTYGQGSGNAATFINNHLLSTLVLDQWNLMRQPRPDSEEFKSIEDKLGINFKIERSIDDIRGKLRQLVLLAQPGYLSGGVEPEQSSPTVELDLLGWSATYSKDLGIYVPVLDKERLFCSAAYPKGVENKSLKSKVGIEQAYKVVRYEALRLVGGWNYPLLNKACKNNAGAARRHLEAKGFPLDEFLAEWSELSEFGEAFEGFNIKLTVTSESLAELNKPVPPKPPNVNRPVNTGGLKAVSNALKTGRYRNEAGLSGLVLLATARSRLQDAVKAKAEAEKLHKSKPDDPDADWFERSETLSDLLEKADIASKVAHSALVETSDALEAV 804
               SCOP domains d2r70a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------2r70A01 A:46-114,A:168-360,A:418-485,A:792-   804                    2r70A02 A:115-167 Helix hairpin bin                  2r70A01 A:46-114,A:168-360,A:418-485,A:792-804 I       nfectious bursa      l virus vp1 polymerase domain                                                                                        ---------------------------------------------------------2r70A01 A:46-114,A:168-360,A:418-485,A:792-804                      -----------------------------------------------------------------------------------------------------------------------       -------------------------------------------------------------------------------------------------------------------------------------------------------   --------------------------2r70A01       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhh.........eeeeeeeehhhhhhhhhhhhhh---....eeeeeeeeeee....................hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhheeee..hhhhhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhh.....-------.....hhhh.eee..------.eee..................hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.eeeeee..eeee.hhh.....eeee.hhhhhhhhhhhhhhhhh......................hhhhhhhhhhhh....eeeee..eeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhee..ee..hhhhhhhhhhhhhhhhh..eeee..eeee.........hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhh.................eeeee..eeeeee....eeeeeehhhhhhhhhhh.....-------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhh.hhhhhh........hhhhhhhhhh................hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..---..hhhhhhhhhhhhhhhh........hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RDRP_DSRNA_BIR  PDB: A:398-598 UniProt: 398-598                                                                                                                                                          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r70 A  27 DVEELLIPKVWVPPEDPLASPSRLAKFLRENGYKVLQPRSLPENEEYETDQILPDLAWMRQI---VLKPTLSLPIGDQEYFPKYYPTHRPSKEKPNAYPPDIALLKQMIYLFLQVPEANEGLKDEVTLLTQNIRDKAYGSGTYMGQANRLVAMKEVATGRNPNKDPLKLGYTFESIAQLLDITLPVGPP-------VPLTRVPSRMLVLTG------EVEDYLPKINLKSSSGLPYVGRTKGETIGEMIAISNQFLRELSTLLKQGAGTKGSNKKKLLSMLSDYWYLSCGLLFPKAERYDKSTWLTKTRNIWSAPSPTHLMISMITWPVMSNSPNNVLNIEGCPSLYKFNPFRGGLNRIVEWILAPEEPKALVYADNIYIVHSNTWYSIDLEKGEANCTRQHMQAAMYYILTRGWSDNGDPMFNQTWATFAMNIAPALVVDSSCLIMNLQIKTYGQGSGNAATFINNHLLSTLVLDQWNLMRQPRPDSEEFKSIEDKLGINFKIERSIDDIRGKLRQLVLLAQPGYLSGGVEPEQSSPTVELDLLGWSATYSKDLGIYVPVLDKERLFCSAAYPKGVE-------VGIEQAYKVVRYEALRLVGGWNYPLLNKACKNNAGAARRHLEAKGFPLDEFLAEWSELSEFGEAFEGFNIKLTVTSESLAELNKPVPPKPPNVNRPVNTGGLKAVSNALKTGRYRNEAGLSGLVLLATARSRLQDAVKAKAEAEKLHKSKP---DADWFERSETLSDLLEKADIASKVAHSALVETSDALEAV 804
                                    36        46        56        66        76        86 |   |  96       106       116       126       136       146       156       166       176       186       196       206        |-      |226       236|      246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       | -     | 616       626       636       646       656       666       676       686       696       706       716       726       736       746       756     | 766       776       786       796        
                                                                                        88  92                                                                                                                        215     223           237    244                                                                                                                                                                                                                                                                                                                                                                     604     612                                                                                                                                                   762 766
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2R70)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RDRP_IBDV | Q9Q6Q5)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
    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: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:0018144    RNA-protein covalent cross-linking    The formation of a covalent cross-link between RNA and a protein.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
cellular component
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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  Cis Peptide Bonds
    Arg A:115 - Pro A:116   [ RasMol ]  
    Glu A:394 - Pro A:395   [ RasMol ]  
    Leu A:260 - Pro A:261   [ RasMol ]  
    Lys A:761 - Pro A:762   [ RasMol ]  
    Thr A:295 - Lys A:296   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        RDRP_IBDV | Q9Q6Q5: 2pgg 2pus 2qj1 2r72

(-) Related Entries Specified in the PDB File

2pus IBDV VP1 POLYMERASE, APO FORM
2qj1 IBDV VP1 POLYMERASE, CRYSTAL SOAKED WITH A PEPTIDE MIMICKING THE VP3 C-TERMINUS.
2r72