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(-) Description

Title :  EPSTEIN-BARR VIRUS PROTEASE
 
Authors :  M. Buisson, J. Hernandez, D. Lascoux, G. Schoehn, E. Forest, G. Arlaud, J. Seigneurin, R. W. H. Ruigrok, W. P. Burmeister
Date :  13 Sep 02  (Deposition) - 14 Nov 02  (Release) - 17 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Proteinase, Beta-Barrel, Hydrolase, Serine Protease, Structural Proteomics In Europe, Spine, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Buisson, J. Hernandez, D. Lascoux, G. Schoehn, E. Forest, G. Arlaud, J. Seigneurin, R. W. H. Ruigrok, W. P. Burmeister
The Crystal Structure Of The Epstein-Barr Virus Protease Shows Rearrangement Of The Processed C Terminus
J. Mol. Biol. V. 324 89 2002
PubMed-ID: 12421561  |  Reference-DOI: 10.1016/S0022-2836(02)01040-9

(-) Compounds

Molecule 1 - CAPSID PROTEIN P40
    Cell Line: B95-8 MARMOSET CELL LINE
    Chains: A, B
    EC Number: 3.4.21.97
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: COAT PROTEIN VP24 (PROTEASE) DOMAIN, RESIDUES 1-235
    Mutation: YES
    Organism Common: HUMAN HERPESVIRUS 4
    Organism Scientific: HUMAN HERPESVIRUS 4
    Organism Taxid: 10376
    Strain: B95-8
    Synonym: ASSEMBLIN, VIRION STRUCTURAL PROTEIN BVRF2, EC-RF3 AND EC-RF3A, PROTEASE, CAPSID PROTEIN VP22A

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ISP2Ligand/IonPHOSPHORYLISOPROPANE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ISP4Ligand/IonPHOSPHORYLISOPROPANE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:25 , HIS A:48 , SER A:116 , LEU A:117 , ILE A:124 , GLY A:146 , ARG A:147 , ARG A:148BINDING SITE FOR RESIDUE ISP A1236
2AC2SOFTWAREHIS B:48 , SER B:116 , LEU B:117 , ALA B:118 , GLY B:146 , ARG B:147 , HOH B:2006BINDING SITE FOR RESIDUE ISP B1236

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O6E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1O6E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O6E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O6E)

(-) Exons   (0, 0)

(no "Exon" information available for 1O6E)

(-) 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:225
 aligned with SCAF_EBVB9 | P03234 from UniProtKB/Swiss-Prot  Length:605

    Alignment length:232
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233  
           SCAF_EBVB9     4 APSVYVCGFVERPDAPPKDACLHLDPLTVKSQLPLKKPLPLTVEHLPDAPVGSVFGLYQSRAGLFSAASITSGDFLSLLDSIYHDCDIAQSQRLPLPREPKVEALHAWLPSLSLASLHPDIPQTTADGGKLSFFDHVSICALGRRRGTTAVYGTDLAWVLKHFSDLEPSIAAQIENDANAAKRESGCPEDHPLPLTKLIAKAIDAGFLRNRVETLRQDRGVANIPAESYLKA 235
               SCOP domains d1o6ea_ A: Epstein-Barr virus protease                                                                                                                                                                                                   SCOP domains
               CATH domains 1o6eA00 A:4-235 Serine Protease, Human Cytomegalovirus Protease; Chain A                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.............hhhhhhhhh.....eeeee..eeeeeeeeeeeeee....eeeeeee.hhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhh.eeeeeee...............eeeeeeee..........eee.hhhhhhhh....hhhhhhhhhhhhhhhh.-------...hhhhhhhhhhhh....hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o6e A   4 APSVYVCGFVERPDAPPKDACLHLDPLTVKSQLPLKKPLPLTVEHLPDAPVGSVFGLYQSSAGLFSAASITSGDFLSLLDSIYHDCDIAQSQRLPLPREPKVEALHAWLPSLSLASLHPDIPQTTADGGKLSFFDHVSICALGRRRGTTAVYGTDLAWVLKHFSDLEPSIAAQIENDANAAKR-------HPLPLTKLIAKAIDAGFLRNRVETLRQDRGVANIPAESYLKA 235
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183  |      -|      203       213       223       233  
                                                                                                                                                                                                                186     194                                         


Chain B from PDB  Type:PROTEIN  Length:232
 aligned with SCAF_EBVB9 | P03234 from UniProtKB/Swiss-Prot  Length:605

    Alignment length:232
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233  
           SCAF_EBVB9     4 APSVYVCGFVERPDAPPKDACLHLDPLTVKSQLPLKKPLPLTVEHLPDAPVGSVFGLYQSRAGLFSAASITSGDFLSLLDSIYHDCDIAQSQRLPLPREPKVEALHAWLPSLSLASLHPDIPQTTADGGKLSFFDHVSICALGRRRGTTAVYGTDLAWVLKHFSDLEPSIAAQIENDANAAKRESGCPEDHPLPLTKLIAKAIDAGFLRNRVETLRQDRGVANIPAESYLKA 235
               SCOP domains d1o6eb_ B: Epstein-Barr virus protease                                                                                                                                                                                                   SCOP domains
               CATH domains 1o6eB00 B:4-235 Serine Protease, Human Cytomegalovirus Protease; Chain A                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.............hhhhhhhhh.....eeeee..eeeeeeeeeeeee.....eeeeeee.hhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhh.eeeeeee...............eeeeeeee..........eee.hhhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhh.....hhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o6e B   4 APSVYVCGFVERPDAPPKDACLHLDPLTVKSQLPLKKPLPLTVEHLPDAPVGSVFGLYQSSAGLFSAASITSGDFLSLLDSIYHDCDIAQSQRLPLPREPKVEALHAWLPSLSLASLHPDIPQTTADGGKLSFFDHVSICALGRRRGTTAVYGTDLAWVLKHFSDLEPSIAAQIENDANAAKRESGCPEDHPLPLTKLIAKAIDAGFLRNRVETLRQDRGVANIPAESYLKA 235
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
   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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1O6E)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SCAF_EBVB9 | P03234)
molecular function
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
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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