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(-) Description

Title :  EPSTEIN-BARR VIRUS ALKALINE NUCLEASE
 
Authors :  M. Buisson, T. Geoui, D. Flot, N. Tarbouriech, W. P. Burmeister
Date :  21 Nov 08  (Deposition) - 30 Jun 09  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Exonuclease, Endonuclease, Gamma-Herpesvirus, Ebv, Bglf5, Dnase, Nuclease, Hydrolase, Herpesvirus, Epstein-Barr Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Buisson, T. Geoui, D. Flot, N. Tarbouriech, M. E. Ressing, E. J. Wiertz, W. P. Burmeister
A Bridge Crosses The Active Site Canyon Of The Epstein-Barr Virus Nuclease With Dnase And Rnase Activity.
J. Mol. Biol. V. 391 717 2009
PubMed-ID: 19538972  |  Reference-DOI: 10.1016/J.JMB.2009.06.034

(-) Compounds

Molecule 1 - ALKALINE EXONUCLEASE
    Chains: A, B
    EC Number: 3.1.11.-
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH FIVE
    Expression System Plasmid: PFASTBAC HTB
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Organism Common: EPSTEIN-BARR VIRUS
    Organism Scientific: HUMAN HERPESVIRUS 4
    Organism Taxid: 10376
    Strain: B95-8
    Synonym: NUCLEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2W45)

(-) Sites  (0, 0)

(no "Site" information available for 2W45)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W45)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W45)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W45)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W45)

(-) Exons   (0, 0)

(no "Exon" information available for 2W45)

(-) 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:449
 aligned with AN_EBVB9 | P03217 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:460
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466
             AN_EBVB9     7 LEDPMEEMTSYTFARFLRSPETEAFVRNLDRPPQMPAMRFVYLYCLCKQIQEFSGETGFCDFVSSLVQENDSKDGPSLKSIYWGLQEATDEQRTVLCSYVESMTRGQSENLMWDILRNGIISSSKLLSTIKNGPTKVFEPAPISTNHYFGGPVAFGLRCEDTVKDIVCKLICGDASANRQFGFMISPTDGIFGVSLDLCVNVESQGDFILFTDRSCIYEIKCRFKYLFSKSEFDPIYPSYTALYKRPCKRSFIRFINSIARPTVEYVPDGRLPSEGDYLLTQDEAWNLKDVRKRKLGPGHDLVADSLAANRGVESMLYVMTDPSENAGRIGIKDRVPVNIFINPRHNYFYQVLLQYKIVGDYVRHSGGGKPGRDCSPRVNIVTAFFRKRSPLDPATCTLGSDLLLDASVEIPVAVLVTPVVLPDSVIRKTLSTAAGSWKAYADNTFDTAPWVPSGLFADD 466
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.....hhhhhhhhhh...----...hhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhh..ee..hhhhhhhhhhhhhhh..-------..hhhhhhhhhhhhhhhhhhhh......ee.....ee......eee...eeeeeeee..eeeeeeeeeeeeeee.hhhh........hhhhhhhhhhh.hhhhhhhhhh......eee............eee.hhhhh............hhhhhhhhhhhh..eeeeeee........ee.eeeeeeee.ee...hhhhhhhhhhhhhhhhhhhh............eeeeeeeeee..........ee...ee......eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh........hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w45 A   7 LEDPMEEMTSYTFARFLRSPETEAFVRNLDRPPQMPAMRFVYLYCLCKQIQEFSGETGFCDFVSSLVQE----DGPSLKSIYWGLQEATDEQRTVLCSYVESMTRGQSENLMWDILRNGIISSSKLLSTIKNGPTKVFEPA-------FGGPVAFGLRCEDTVKDIVCKLICGDASANRQFGFMISPTDGIFGVSLDLCVNVESQGDFILFTDRSCIYEIKCRFKYLFSKSEFDPIYPSYTALYKRPCKRSFIRFINSIARPTVEYVPDGRLPSEGDYLLTQDEAWNLKDVRKRKLGPGHDLVADSLAANRGVESMLYVMTDPSENAGRIGIKDRVPVNIFINPRHNYFYQVLLQYKIVGDYVRHSGGGKPGRDCSPRVNIVTAFFRKRSPLDPATCTLGSDLLLDASVEIPVAVLVTPVVLPDSVIRKTLSTAAGSWKAYADNTFDTAPWVPSGLFADD 466
                                    16        26        36        46        56        66        |-   |    86        96       106       116       126       136       146|      156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466
                                                                                               75   80                                                                147     155                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:437
 aligned with AN_EBVB9 | P03217 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:455
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457     
             AN_EBVB9     8 EDPMEEMTSYTFARFLRSPETEAFVRNLDRPPQMPAMRFVYLYCLCKQIQEFSGETGFCDFVSSLVQENDSKDGPSLKSIYWGLQEATDEQRTVLCSYVESMTRGQSENLMWDILRNGIISSSKLLSTIKNGPTKVFEPAPISTNHYFGGPVAFGLRCEDTVKDIVCKLICGDASANRQFGFMISPTDGIFGVSLDLCVNVESQGDFILFTDRSCIYEIKCRFKYLFSKSEFDPIYPSYTALYKRPCKRSFIRFINSIARPTVEYVPDGRLPSEGDYLLTQDEAWNLKDVRKRKLGPGHDLVADSLAANRGVESMLYVMTDPSENAGRIGIKDRVPVNIFINPRHNYFYQVLLQYKIVGDYVRHSGGGKPGRDCSPRVNIVTAFFRKRSPLDPATCTLGSDLLLDASVEIPVAVLVTPVVLPDSVIRKTLSTAAGSWKAYADNTFDTAPWVPSGL 462
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh....hhhhhhhhhh.-------..hhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhh....ee..hhhhhhhhhhhhhhh.--------..hhhhhhhhhhhhhhhhhhh..............ee......eee...eeeeee......eeeeeeeeeeeee.hhhhee......hhhhhhhhhhh.hhhhhhhhhh......eee............eee.hhhhh............hhhhhhhhhhhh...eeeeee.hhhhh..ee.eeeeeee..ee...hhhhhhhhhhhhhhhhhhhh.....---....eeeeeeeeeee.........ee...........eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w45 B   8 EDPMEEMTSYTFARFLRSPETEAFVRNLDRPPQMPAMRFVYLYCLCKQIQEFSGETGFCDFVSSLV-------GPSLKSIYWGLQEATDEQRTVLCSYVESMTRGQSENLMWDILRNGIISSSKLLSTIKNGPTKVFEP--------FGGPVAFGLRCEDTVKDIVCKLICGDASANRQFGFMISPTDGIFGVSLDLCVNVESQGDFILFTDRSCIYEIKCRFKYLFSKSEFDPIYPSYTALYKRPCKRSFIRFINSIARPTVEYVPDGRLPSEGDYLLTQDEAWNLKDVRKRKLGPGHDLVADSLAANRGVESMLYVMTDPSENAGRIGIKDRVPVNIFINPRHNYFYQVLLQYKIVGDYVRHSGGGK---DCSPRVNIVTAFFRKRSPLDPATCTLGSDLLLDASVEIPVAVLVTPVVLPDSVIRKTLSTAAGSWKAYADNTFDTAPWVPSGL 462
                                    17        27        37        47        57        67     |   -   |    87        97       107       117       127       137        |-       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367        |-  |    387       397       407       417       427       437       447       457     
                                                                                            73      81                                                              146      155                                                                                                                                                                                                                          376 380
   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 2W45)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W45)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2W45)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (AN_EBVB9 | P03217)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0039595    induction by virus of catabolism of host mRNA    The process in which a virus increases the frequency, rate or extent of the breakdown of host messenger RNA (mRNA).
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0039657    suppression by virus of host gene expression    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AN_EBVB9 | P03217: 2w4b

(-) Related Entries Specified in the PDB File

2w4b EPSTEIN-BARR VIRUS ALCALINE NUCLEASE D203S MUTANT