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(-) Description

Title :  N-TERMINAL ENDONUCLEASE DOMAIN OF LA CROSSE VIRUS L-PROTEIN
 
Authors :  J. Reguera, F. Weber, S. Cusack
Date :  28 Jun 10  (Deposition) - 06 Oct 10  (Release) - 18 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Transferase, Bunyaviridae, Orthobunyavirus, Aedes Triseriatus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Reguera, F. Weber, S. Cusack
Bunyaviridae Rna Polymerases (L-Protein) Have An N-Terminal Influenza-Like Endonuclease Domain, Essential For Viral Cap Dependent Transcription.
Plos Pathog. V. 6 1101 2010
PubMed-ID: 20862319  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1001101

(-) Compounds

Molecule 1 - RNA POLYMERASE L
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET9A
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL ENDONUCLEASE DOMAIN, RESIDUES 1-183
    Organism Scientific: BUNYAVIRUS LA CROSSE
    Organism Taxid: 11577
    Synonym: L-PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:34 , ASP A:79 , ASP A:92 , TYR A:93 , HOH A:2110 , HOH A:2111BINDING SITE FOR RESIDUE MN A1184
2AC2SOFTWAREHIS B:34 , ASP B:79 , ASP B:92 , TYR B:93 , HOH B:2129 , HOH B:2130BINDING SITE FOR RESIDUE MN B1184
3AC3SOFTWAREHIS C:34 , ASP C:79 , ASP C:92 , TYR C:93 , HOH C:2097 , HOH C:2098BINDING SITE FOR RESIDUE MN C1184
4AC4SOFTWAREHIS D:34 , ASP D:79 , ASP D:92 , TYR D:93 , HOH D:2125 , HOH D:2126BINDING SITE FOR RESIDUE MN D1184

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XI5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XI5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XI5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XI5)

(-) Exons   (0, 0)

(no "Exon" information available for 2XI5)

(-) 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:184
 aligned with A5HC98_BUNLC | A5HC98 from UniProtKB/TrEMBL  Length:2263

    Alignment length:184
                             1                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    
         A5HC98_BUNLC     - -MDYQEYQQFLARINTARDACVAKDIDVDLLMARHDYFGRELCKSLNIEYRNDVPFIDIILDIRPEVDPLTIDAPHITPDNYLYINNVLYIIDYKVSVSNESSVITYDKYYELTRDISDRLSIPIEIVIIRIDPVSRDLHINSDRFKELYPTIVVDINFNQFFDLKQLLYEKFGDDEEFLLKVA 183
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh................eeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......eee.hhhhhhhh........hhhhhhhhhhhhhhhh.hhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xi5 A   0 GMDYQEYQQFLARINTARDACVAKDIDVDLLMARHDYFGRELCKSLNIEYRNDVPFIDIILDIRPEVDPLTIDAPHITPDNYLYINNVLYIIDYKVSVSNESSVITYDKYYELTRDISDRLSIPIEIVIIRIDPVSRDLHINSDRFKELYPTIVVDINFNQFFDLKQLLYEKFGDDEEFLLKVA 183
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    


Chain B from PDB  Type:PROTEIN  Length:184
 aligned with A5HC98_BUNLC | A5HC98 from UniProtKB/TrEMBL  Length:2263

    Alignment length:184
                             1                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    
         A5HC98_BUNLC     - -MDYQEYQQFLARINTARDACVAKDIDVDLLMARHDYFGRELCKSLNIEYRNDVPFIDIILDIRPEVDPLTIDAPHITPDNYLYINNVLYIIDYKVSVSNESSVITYDKYYELTRDISDRLSIPIEIVIIRIDPVSRDLHINSDRFKELYPTIVVDINFNQFFDLKQLLYEKFGDDEEFLLKVA 183
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh................eeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......eee.hhhhhhhh........hhhhhhhhhhhhhhhh.hhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xi5 B   0 GMDYQEYQQFLARINTARDACVAKDIDVDLLMARHDYFGRELCKSLNIEYRNDVPFIDIILDIRPEVDPLTIDAPHITPDNYLYINNVLYIIDYKVSVSNESSVITYDKYYELTRDISDRLSIPIEIVIIRIDPVSRDLHINSDRFKELYPTIVVDINFNQFFDLKQLLYEKFGDDEEFLLKVA 183
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    


Chain C from PDB  Type:PROTEIN  Length:184
 aligned with A5HC98_BUNLC | A5HC98 from UniProtKB/TrEMBL  Length:2263

    Alignment length:184
                             1                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    
         A5HC98_BUNLC     - -MDYQEYQQFLARINTARDACVAKDIDVDLLMARHDYFGRELCKSLNIEYRNDVPFIDIILDIRPEVDPLTIDAPHITPDNYLYINNVLYIIDYKVSVSNESSVITYDKYYELTRDISDRLSIPIEIVIIRIDPVSRDLHINSDRFKELYPTIVVDINFNQFFDLKQLLYEKFGDDEEFLLKVA 183
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh................eeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......eee.hhhhhhhh........hhhhhhhhhhhhhhhh.hhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xi5 C   0 GMDYQEYQQFLARINTARDACVAKDIDVDLLMARHDYFGRELCKSLNIEYRNDVPFIDIILDIRPEVDPLTIDAPHITPDNYLYINNVLYIIDYKVSVSNESSVITYDKYYELTRDISDRLSIPIEIVIIRIDPVSRDLHINSDRFKELYPTIVVDINFNQFFDLKQLLYEKFGDDEEFLLKVA 183
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    


Chain D from PDB  Type:PROTEIN  Length:184
 aligned with A5HC98_BUNLC | A5HC98 from UniProtKB/TrEMBL  Length:2263

    Alignment length:184
                             1                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    
         A5HC98_BUNLC     - -MDYQEYQQFLARINTARDACVAKDIDVDLLMARHDYFGRELCKSLNIEYRNDVPFIDIILDIRPEVDPLTIDAPHITPDNYLYINNVLYIIDYKVSVSNESSVITYDKYYELTRDISDRLSIPIEIVIIRIDPVSRDLHINSDRFKELYPTIVVDINFNQFFDLKQLLYEKFGDDEEFLLKVA 183
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh................eeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......eee.hhhhhhhh........hhhhhhhhhhhhhhh..hhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xi5 D   0 GMDYQEYQQFLARINTARDACVAKDIDVDLLMARHDYFGRELCKSLNIEYRNDVPFIDIILDIRPEVDPLTIDAPHITPDNYLYINNVLYIIDYKVSVSNESSVITYDKYYELTRDISDRLSIPIEIVIIRIDPVSRDLHINSDRFKELYPTIVVDINFNQFFDLKQLLYEKFGDDEEFLLKVA 183
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
   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  (0, 0)

(no "SCOP Domain" information available for 2XI5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XI5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XI5)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A5HC98_BUNLC | A5HC98)
molecular function
    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: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: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.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.

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 Related Entries

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

UniProtKB/TrEMBL
        A5HC98_BUNLC | A5HC98: 2xi7 5amq 5amr

(-) Related Entries Specified in the PDB File

2xi7 N-TERMINAL ENDONUCLEASE DOMAIN OF LA CROSSE VIRUS L-PROTEIN