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(-) Description

Title :  STRUCTURE OF D212, A NUCLEASE FROM A FUSSELOVIRUS.
 
Authors :  S. K. Menon, M. J. Young, C. M. Lawrence
Date :  17 Jan 09  (Deposition) - 03 Feb 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ssv1, Crenarchaeal Virus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. K. Menon, B. J. Eilers, M. J. Young, C. M. Lawrence
The Crystal Structure Of D212 From Sulfolobus Spindle-Shaped Virus Ragged Hills Reveals A New Member Of The Pd-(D/E)Xk Nuclease Superfamily.
J. Virol. V. 84 5890 2010
PubMed-ID: 20375162  |  Reference-DOI: 10.1128/JVI.01663-09

(-) Compounds

Molecule 1 - ORF D212
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEXP14-SSVRH D212
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PDEST14
    Expression System Vector Type: PLASMID
    Organism Scientific: SULFOLOBUS VIRUS RAGGED HILLS
    Organism Taxid: 256994
    Synonym: D212

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2W8M)

(-) Sites  (0, 0)

(no "Site" information available for 2W8M)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W8M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W8M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W8M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W8M)

(-) Exons   (0, 0)

(no "Exon" information available for 2W8M)

(-) 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:165
 aligned with Q6TRV5_9VIRU | Q6TRV5 from UniProtKB/TrEMBL  Length:212

    Alignment length:189
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198         
         Q6TRV5_9VIRU    19 ILPTVGLGREYLVLGKLLISLSKWRAKGLIDFDVYLRPTGVGTLTNTINYEYYKGLEDKYDLTLYIRAKDSYYPLLWIDITGSSWTEEQSKERYGESIYAILSVKVETAKKYDVLGRVFFIHYNDTEDKLKCISALQILNLERQNKIKKDKFERGAKSEYYLIPTSYWKNLTELRIALRGFYQSFKEYL 207
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhh.........-------------...hhhhh....eeeeee....eeeeeeeee.........-----...eeeeehhhhhhhhhh.....eeeeeee....eeeeeehhhhhhhhhh....ee.------..eeeee.hhheehhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w8m A  19 ILPTVGLGREYLVLGKLLISLSKWRAKGLIDFDVYL-------------YEYYKGLEDKYDLTLYIRAKDSYYPLLWIDITGSSWTEEQ-----GESIYAILSVKVETAKKYDVLGRVFFIHYNDTEDKLKCISALQILNLERQNKIKKDK------SEYYLIPTSYWKNLTELRIALRGFYQSFKEYL 207
                                    28        38        48     |   -        68        78        88        98        |-    |  118       128       138       148       158       168|      178       188       198         
                                                              54            68                                    107   113                                                     169    176                               


Chain B from PDB  Type:PROTEIN  Length:168
 aligned with Q6TRV5_9VIRU | Q6TRV5 from UniProtKB/TrEMBL  Length:212

    Alignment length:188
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196        
         Q6TRV5_9VIRU    17 DYILPTVGLGREYLVLGKLLISLSKWRAKGLIDFDVYLRPTGVGTLTNTINYEYYKGLEDKYDLTLYIRAKDSYYPLLWIDITGSSWTEEQSKERYGESIYAILSVKVETAKKYDVLGRVFFIHYNDTEDKLKCISALQILNLERQNKIKKDKFERGAKSEYYLIPTSYWKNLTELRIALRGFYQSFK 204
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) VirArc_Nuclease-2w8mB01 B:17-194                                                                                                                                                  ---------- Pfam domains (1)
           Pfam domains (2) VirArc_Nuclease-2w8mB02 B:17-194                                                                                                                                                  ---------- Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhh.......eeee.----------...hhhhh....eeeeeee..eeeeeeeeee.-------hhhhhhh..eeeeehhhhhhhhhh.....eeeeeee....eeeeeehhhhhhhhhh...eeee..---..eeeeee.hhheehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w8m B  17 DYILPTVGLGREYLVLGKLLISLSKWRAKGLIDFDVYLRPT----------YEYYKGLEDKYDLTLYIRAKDSYYPLLWIDIT-------QSKERYGESIYAILSVKVETAKKYDVLGRVFFIHYNDTEDKLKCISALQILNLERQNKIKKDKFE---KSEYYLIPTSYWKNLTELRIALRGFYQSFK 204
                                    26        36        46        56|        - |      76        86        96  |      -|      116       126       136       146       156       166    |  176       186       196        
                                                                   57         68                             99     107                                                             171 175
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  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 2W8M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W8M)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: VirArc_Nuclease] (1)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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