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(-) Description

Title :  CRYSTAL STRUCTURE OF A BIRNAVIRUS (IBDV) RNA-DEPENDENT RNA POLYMERASE VP1
 
Authors :  J. Pan, V. N. Vakharia, Y. J. Tao
Date :  09 Apr 07  (Deposition) - 22 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Polymerase, Rdrp, Birnavirus, Ibdv, Permutation, Dsrna Virus, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Pan, V. N. Vakharia, Y. J. Tao
The Structure Of A Birnavirus Polymerase Reveals A Distinct Active Site Topology.
Proc. Natl. Acad. Sci. Usa V. 104 7385 2007
PubMed-ID: 17456597  |  Reference-DOI: 10.1073/PNAS.0611599104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA-DIRECTED RNA POLYMERASE
    Chains: A
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Strain: SF21
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: VP1
    Organism Common: GUMBORO VIRUS
    Organism Scientific: INFECTIOUS BURSAL DISEASE VIRUS
    Organism Taxid: 10995
    Strain: D78
    Synonym: RDRP, PROTEIN VP1

 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 2PGG)

(-) Sites  (0, 0)

(no "Site" information available for 2PGG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:115 -Pro A:116
2Glu A:394 -Pro A:395

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 2PGG)

(-) 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:765
 aligned with RDRP_IBDV | Q9Q6Q5 from UniProtKB/Swiss-Prot  Length:881

    Alignment length:774
                                    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       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800    
            RDRP_IBDV    31 LLIPKVWVPPEDPLASPSRLAKFLRENGYKVLQPRSLPENEEYETDQILPDLAWMRQIEGAVLKPTLSLPIGDQEYFPKYYPTHRPSKEKPNAYPPDIALLKQMIYLFLQVPEANEGLKDEVTLLTQNIRDKAYGSGTYMGQATRLVAMKEVATGRNPNKDPLKLGYTFESIAQLLDITLPVGPPGEDDKPWVPLTRVPSRMLVLTGDVDGDFEVEDYLPKINLKSSSGLPYVGRTKGETIGEMIAISNQFLRELSTLLKQGAGTKGSNKKKLLSMLSDYWYLSCGLLFPKAERYDKSTWLTKTRNIWSAPSPTHLMISMITWPVMSNSPNNVLNIEGCPSLYKFNPFRGGLNRIVEWILAPEEPKALVYADNIYIVHSNTWYSIDLEKGEANCTRQHMQAAMYYILTRGWSDNGDPMFNQTWATFAMNIAPALVVDSSCLIMNLQIKTYGQGSGNAATFINNHLLSTLVLDQWNLMRQPRPDSEEFKSIEDKLGINFKIERSIDDIRGKLRQLVLLAQPGYLSGGVEPEQSSPTVELDLLGWSATYSKDLGIYVPVLDKERLFCSAAYPKGVENKSLKSKVGIEQAYKVVRYEALRLVGGWNYPLLNKACKNNAGAARRHLEAKGFPLDEFLAEWSELSEFGEAFEGFNIKLTVTSESLAELNKPVPPKPPNVNRPVNTGGLKAVSNALKTGRYRNEAGLSGLVLLATARSRLQDAVKAKAEAEKLHKSKPDDPDADWFERSETLSDLLEKADIASKVAHSALVETSDALEAV 804
               SCOP domains d2pgga1 A:31-804 Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------2pggA01 A:46-114,A:168-360,A:418-485,A:792-804                       2pggA02 A:115-167 Helix hairpin bin                  2pggA01 A:46-114,A:168-360,A:418-485,A:792-804 Infectious bursal virus vp1 polymerase domain                                                                                                     ---------------------------------------------------------2pggA01 A:46-114,A:168-360,A:418-485,A:792-804                      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2pggA01       CATH domains
               Pfam domains Birna_RdRp-2pggA01 A:31-804                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhh.........ee..eeeehhhhh..hhhhhh........eeee.....ee....................hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhheeee..hhhhhhhhhhhhhhhhh......hhhhh..hhhhhhhhhhhhh.................hhhh.eee.........eee...........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.eeeeee..eeee.hhh.....eeee.hhhhhhhhhhhhhhhhh......................hhhhhhhhhhhh....eeeee..eeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhee..ee..hhhhhhhhhhhhhhhhh..eeee..eeee.........hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhh.................eeeee..eeeee......eeeeehhhhhhhhhhh...---------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhh................hhhhhhhhhhh......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RDRP_DSRNA_BIR  PDB: A:398-598 UniProt: 398-598                                                                                                                                                          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pgg A  31 LLIPKVWVPPEDPLASPSRLAKFLRENGYKVLQPRSLPENEEYETDQILPDLAWMRQIEGAVLKPTLSLPIGDQEYFPKYYPTHRPSKEKPNAYPPDIALLKQMIYLFLQVPEANEGLKDEVTLLTQNIRDKAYGSGTYMGQATRLVAMKEVATGRNPNKDPLKLGYTFESIAQLLDITLPVGPPGEDDKPWVPLTRVPSRMLVLTGDVDGDFEVEDYLPKINLKSSSGLPYVGRTKGETIGEMIAISNQFLRELSTLLKQGAGTKGSNKKKLLSMLSDYWYLSCGLLFPKAERYDKSTWLTKTRNIWSAPSPTHLMISMITWPVMSNSPNNVLNIEGCPSLYKFNPFRGGLNRIVEWILAPEEPKALVYADNIYIVHSNTWYSIDLEKGEANCTRQHMQAAMYYILTRGWSDNGDPMFNQTWATFAMNIAPALVVDSSCLIMNLQIKTYGQGSGNAATFINNHLLSTLVLDQWNLMRQPRPDSEEFKSIEDKLGINFKIERSIDDIRGKLRQLVLLAQPGYLSGGVEPEQSSPTVELDLLGWSATYSKDLGIYVPVLDKERLFCSAAYPKG---------VGIEQAYKVVRYEALRLVGGWNYPLLNKACKNNAGAARRHLEAKGFPLDEFLAEWSELSEFGEAFEGFNIKLTVTSESLAELNKPVPPKPPNVNRPVNTGGLKAVSNALKTGRYRNEAGLSGLVLLATARSRLQDAVKAKAEAEKLHKSKPDDPDADWFERSETLSDLLEKADIASKVAHSALVETSDALEAV 804
                                    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       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600 |       - |     620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     602       612
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Birna_RdRp] (3)

(-) 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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        RDRP_IBDV | Q9Q6Q5: 2pus 2qj1 2r70 2r72

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