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(-) Description

Title :  NORWALK VIRUS POLYMERASE BOUND TO CYTIDINE 5'-TRIPHOSPHATE AND PRIMER-TEMPLATE RNA
 
Authors :  D. F. Zamyatkin, K. K. S. Ng
Date :  26 Dec 07  (Deposition) - 08 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Rna-Dependent Rna Polymerase, Viral Replication, Antiviral Enzyme Inhibitor, Helicase, Hydrolase, Nucleotide-Binding, Nucleotidyltransferase, Rna Replication, Rna-Directed Rna Polymerase, Transferase, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. F. Zamyatkin, F. Parra, J. M. Alonso, D. A. Harki, B. R. Peterson, P. Grochulski, K. K. Ng
Structural Insights Into Mechanisms Of Catalysis And Inhibition In Norwalk Virus Polymerase.
J. Biol. Chem. V. 283 7705 2008
PubMed-ID: 18184655  |  Reference-DOI: 10.1074/JBC.M709563200

(-) Compounds

Molecule 1 - RNA DEPENDENT RNA POLYMERASE
    Chains: A
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-2T
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: POLYMERASE
    Organism Scientific: NORWALK VIRUS
    Organism Taxid: 11983
    Strain: AST6139/01/SP
 
Molecule 2 - RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3')
    Chains: P
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED SELF-COMPLEMENTARY RNA OLIGONUCLEOTIDE WITH 2-BASE OVERHANG
    Synthetic: YES
 
Molecule 3 - RNA (5'-R(P*UP*GP*CP*CP*CP*GP*GP*GP*C)-3')
    Chains: T
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED SELF-COMPLEMENTARY RNA OLIGONUCLEOTIDE THAT WAS EXTENDED BY A SINGLE CYTIDINE 5'- MONOPHOSPHATE RESIDUE DURING CRYSTALLIZATION
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CTP1Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
2GOL4Ligand/IonGLYCEROL
3MN3Ligand/IonMANGANESE (II) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:30 , LEU A:36 , ARG A:52 , SER A:427 , HOH A:627 , HOH A:630 , HOH A:822BINDING SITE FOR RESIDUE GOL A 515
2AC2SOFTWAREALA A:256 , LEU A:259 , GLU A:260 , GLN A:273 , HOH A:669BINDING SITE FOR RESIDUE GOL A 516
3AC3SOFTWAREASP A:242 , ASP A:343 , ASP A:344 , CTP A:514 , HOH A:658 , G P:8BINDING SITE FOR RESIDUE MN A 511
4AC4SOFTWAREASP A:242 , TYR A:243 , ASP A:343 , CTP A:514BINDING SITE FOR RESIDUE MN A 512
5AC5SOFTWAREASP A:99 , GLU A:205 , HIS A:209 , ASP A:289BINDING SITE FOR RESIDUE MN A 513
6AC6SOFTWARELYS A:166 , ARG A:182 , ASP A:242 , TYR A:243 , SER A:244 , ARG A:245 , TRP A:246 , ASP A:247 , SER A:300 , THR A:305 , ASN A:309 , ASP A:343 , MN A:511 , MN A:512 , HOH A:658 , HOH A:722 , HOH A:759 , HOH A:840 , G P:8 , G T:2BINDING SITE FOR RESIDUE CTP A 514
7AC7SOFTWAREPHE A:28 , LEU A:169 , ARG A:413 , GLN A:414 , TRP A:417 , ARG A:419 , HOH A:838 , C P:5 , G P:6 , HOH P:21BINDING SITE FOR RESIDUE GOL P 9
8AC8SOFTWARELYS A:166 , G T:2 , C T:3 , C T:4 , HOH T:11 , HOH T:32 , HOH T:40BINDING SITE FOR RESIDUE GOL T 10

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BSO)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:121 -Pro A:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BSO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BSO)

(-) Exons   (0, 0)

(no "Exon" information available for 3BSO)

(-) 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:479
 aligned with Q70ET3_9CALI | Q70ET3 from UniProtKB/TrEMBL  Length:838

    Alignment length:484
                                   342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812    
         Q70ET3_9CALI   333 KGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDPPDKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKTHCVTLPIRVGMNMNEDGPIIFERHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFS 816
               SCOP domains d3bsoa_ A: Viral RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eeeeee.........eeeee...........ee..............hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhh............hhhhhh.....hhhhhhhhhhhhhhhhhh.....eeeeee...ee.hhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeee...eeeee.........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeee..eeeeee....hhhhhhhhhhhh...ee..................ee..eeeeee..eeeeeehhhhhhh...eeeeeee............hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.-----.....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bso A   5 KGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDPPDKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKTHCVTLPIRVGMNMNEDGPIIFERHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAEL-----DFYVPRQEPMFRWMRFS 488
                                    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    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       466   472                


Chain P from PDB  Type:RNA  Length:7
                                       
                 3bso P   2 GCCCGGG   8


Chain T from PDB  Type:RNA  Length:9
                                         
                 3bso T   1 UGCCCGGGC   9
   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  (0, 0)

(no "CATH Domain" information available for 3BSO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BSO)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q70ET3_9CALI | Q70ET3)
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: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:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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: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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0039694    viral RNA genome replication    The replication of a viral RNA genome.

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 Related Entries

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

UniProtKB/TrEMBL
        Q70ET3_9CALI | Q70ET3: 1sh0 1sh2 1sh3 3bsn 3h5x 3h5y 4qpx 5tsn

(-) Related Entries Specified in the PDB File

1sh0 NORWALK VIRUS POLYMERASE
3bsn NORWALK VIRUS POLYMERASE BOUND TO 5-NITROCYTIDINE-5'- TRIPHOSPHATE AND PRIMER-TEMPLATE RNA