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(-) Description

Title :  CRYSTAL STRUCTURE OF 2'-AMINO-2'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE BOUND TO NOROVIRUS GII RNA POLYMERASE
 
Authors :  D. F. Zamyatkin, F. Parra, A. Machin, P. Grochulski, K. K. S. Ng
Date :  22 Apr 09  (Deposition) - 19 May 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Polymerase-Rna Complex, Non-Natural Nucleoside Triphosphate Analog, Calicivirus, Hydrolase, Nucleotide-Binding, Nucleotidyltransferase, Protease, Rna Replication, Rna-Directed Rna Polymerase, Thiol Protease, Transferase, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. F. Zamyatkin, F. Parra, A. Machin, P. Grochulski, K. K. Ng
Binding Of 2'-Amino-2'-Deoxycytidine-5'-Triphosphate To Norovirus Polymerase Induces Rearrangement Of The Active Site.
J. Mol. Biol. V. 390 10 2009
PubMed-ID: 19426741  |  Reference-DOI: 10.1016/J.JMB.2009.04.069

(-) 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 - 5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3'
    Chains: P
    Engineered: YES
    Other Details: PRIMER RNA
    Synthetic: YES
 
Molecule 3 - 5'-R(P*UP*GP*CP*CP*CP*GP*GP*GP*C)-3'
    Chains: T
    Engineered: YES
    Other Details: TEMPLATE RNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1CSG1Ligand/Ion2'-AMINO-2'-DEOXYCYTIDINE 5'-(TETRAHYDROGENTRIPHOSPHATE)
2GOL4Ligand/IonGLYCEROL
3MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:243 , ASP A:343 , CSG A:515 , HOH A:882BINDING SITE FOR RESIDUE MN A 511
2AC2SOFTWAREASP A:343 , CSG A:515 , G P:8BINDING SITE FOR RESIDUE MN A 512
3AC3SOFTWAREALA A:241 , ASP A:344 , HOH A:563 , HOH A:637BINDING SITE FOR RESIDUE MN A 513
4AC4SOFTWAREASP A:99 , GLU A:205 , HIS A:209 , ASP A:289BINDING SITE FOR RESIDUE MN A 514
5AC5SOFTWAREARG A:182 , TYR A:243 , SER A:244 , ARG A:245 , TRP A:246 , ASP A:247 , SER A:300 , ASN A:309 , ASP A:343 , MN A:511 , MN A:512 , HOH A:738 , HOH A:780 , HOH A:816 , HOH A:883 , HOH A:884 , G P:8 , G T:2BINDING SITE FOR RESIDUE CSG A 515
6AC6SOFTWAREARG A:30 , LEU A:36 , ARG A:52 , SER A:427 , HOH A:635 , HOH A:638BINDING SITE FOR RESIDUE GOL A 516
7AC7SOFTWARELEU A:169 , ARG A:413 , GLN A:414 , TRP A:417 , THR A:418 , ARG A:419 , HOH A:754 , C P:5 , G P:6BINDING SITE FOR RESIDUE GOL A 517
8AC8SOFTWAREALA A:256 , GLU A:260 , GLN A:273 , HOH A:682BINDING SITE FOR RESIDUE GOL A 518
9AC9SOFTWARETHR A:117 , LYS A:166 , G T:2 , C T:3 , C T:4 , HOH T:517 , HOH T:721 , HOH T:814 , HOH T:896BINDING SITE FOR RESIDUE GOL T 509

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H5X)

(-) 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 3H5X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H5X)

(-) Exons   (0, 0)

(no "Exon" information available for 3H5X)

(-) 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:470
 aligned with Q70ET3_9CALI | Q70ET3 from UniProtKB/TrEMBL  Length:838

    Alignment length:483
                                   343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813   
         Q70ET3_9CALI   334 GTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDPPDKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKTHCVTLPIRVGMNMNEDGPIIFERHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFS 816
               SCOP domains d3h5xa_ 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.....hhhhhhhhhhhhhhhhh......eeeeee...ee.hhhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhhh.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
                 3h5x A   6 GTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDPPDKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKTHCVTLPIRVGMNMNEDGPIIFERHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPT-------PLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAE------DFYVPRQEPMFRWMRFS 488
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365    |    -  |    385       395       405       415       425       435       445       455       465      |475       485   
                                                                                                                                                                                                                                                                                                                                                                                                      370     378                                                                                    465    472                


Chain P from PDB  Type:RNA  Length:7
                                       
                 3h5x P   2 GCCCGGG   8


Chain T from PDB  Type:RNA  Length:9
                                         
                 3h5x 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 3H5X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H5X)

(-) 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 3bso 3h5y 4qpx 5tsn

(-) Related Entries Specified in the PDB File

1sh0 THE SAME PROTEIN IN A LIGAND-FREE FORM
3bsn THE SAME PROTEIN BOUND TO 5-NITROCYTIDINE-5'-TRIPHOSPHATE
3bso THE SAME PROTEIN BOUND TO CTP
3h5y