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(-) Description

Title :  CRYSTAL STRUCTURE OF VP4 PROTEASE FROM INFECTIOUS PANCREATIC NECROSIS VIRUS (IPNV) IN SPACE GROUP P6122
 
Authors :  M. Paetzel, J. Lee, A. R. Feldman, B. Delmas
Date :  24 Apr 07  (Deposition) - 05 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Protease, Ser/Lys Dyad, Viral Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Lee, A. R. Feldman, B. Delmas, M. Paetzel
Crystal Structure Of The Vp4 Protease From Infectious Pancreatic Necrosis Virus Reveals The Acyl-Enzyme Complex For An Intermolecular Self-Cleavage Reaction.
J. Biol. Chem. V. 282 24928 2007
PubMed-ID: 17553791  |  Reference-DOI: 10.1074/JBC.M701551200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEASE VP4
    Chains: A
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: VP4HEX (RESIDUES 524-716)
    Mutation: YES
    Organism Scientific: INFECTIOUS PANCREATIC NECROSIS VIRUS - SP
    Organism Taxid: 11005
    Strain: SEROTYPE SP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2PNM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_POLS_IPNVS_027 *P565RPOLS_IPNVS  ---  ---AP565R
2UniProtVAR_POLS_IPNVS_028 *D672APOLS_IPNVS  ---  ---AD672A
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PNM)

(-) 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:181
 aligned with A1XQR0_9VIRU | A1XQR0 from UniProtKB/TrEMBL  Length:972

    Alignment length:188
                                   533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703        
         A1XQR0_9VIRU   524 LESANYEEVELPPPSKGVIVPVVHTVKSAPGEAFGSLAIIIPGEYPELLDANQQVLSHFANDTGSVWGIGEDIPFEGDNMCYTALPLKEIKRNGNIVVEKIFAGPIMGPSAQLGLSLLVNDIEDGVPRMVFTGEIADDEETIIPICGVDIKAIAAHEQGLPLIGNQPGVDEEVRNTSLAAHLIQTGTL 711
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Birna_VP4-2pnmA01 A:524-       706                                                                                                                                                     ----- Pfam domains
         Sec.struct. author ........eee......eeeeeee-------..eeeeeeeee..hhhhhhhhhh.eeeee...eeee.....eeee...eeeeeeeeeee.....eee............hhhhhhhhhhh........ee..ee......ee...hhhhhhhhhhh....eee......ee..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------R----------------------------------------------------------------------------------------------------------A--------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pnm A 524 LESANYEEVELPPPSKGVIVPVVH-------EAFGSLAIIIPGEYPELLDANQQVLSHFANDTGSVWGIGEDIPFEGDNmCYTALPLKEIKRNGNIVVEKIFAGPImGPSAQLGLSLLVNDIEDGVPRmVFTGEIADDEETIIPICGVDIAAIAAHEQGLPLIGNQPGVDEEVRNTSLAAHLIQTGTL 711
                                   533       543   |     - |     563       573       583       593       603       613       623      |633       643       653       663       673       683       693       703        
                                                 547     555                                             603-MSE                    630-MSE               652-MSE                                                       


Chain A from PDB  Type:PROTEIN  Length:181
 aligned with POLS_IPNVS | Q703G9 from UniProtKB/Swiss-Prot  Length:972

    Alignment length:188
                                   533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703        
           POLS_IPNVS   524 LESANYEEVELPPPSKGVIVPVVHTVKSAPGEAFGSLAIIIPGEYPELLDANQQVLSHFANDTGSVWGIGEDIPFEGDNMCYTALPLKEIKRNGNIVVEKIFAGPIMGPSAQLGLSLLVNDIEDGVPRMVFTGEIADDEETIIPICGVDIKAIAAHEQGLPLIGNQPGVDEEVRNTSLAAHLIQTGTL 711
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Birna_VP4-2pnmA01 A:524-       706                                                                                                                                                     ----- Pfam domains
         Sec.struct. author ........eee......eeeeeee-------..eeeeeeeee..hhhhhhhhhh.eeeee...eeee.....eeee...eeeeeeeeeee.....eee............hhhhhhhhhhh........ee..ee......ee...hhhhhhhhhhh....eee......ee..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------R----------------------------------------------------------------------------------------------------------A--------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pnm A 524 LESANYEEVELPPPSKGVIVPVVH-------EAFGSLAIIIPGEYPELLDANQQVLSHFANDTGSVWGIGEDIPFEGDNmCYTALPLKEIKRNGNIVVEKIFAGPImGPSAQLGLSLLVNDIEDGVPRmVFTGEIADDEETIIPICGVDIAAIAAHEQGLPLIGNQPGVDEEVRNTSLAAHLIQTGTL 711
                                   533       543   |     - |     563       573       583       593       603       613       623      |633       643       653       663       673       683       693       703        
                                                 547     555                                             603-MSE                    630-MSE               652-MSE
   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 2PNM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Birna_VP4] (2)

(-) Gene Ontology  (9, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A1XQR0_9VIRU | A1XQR0)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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).
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

Chain A   (POLS_IPNVS | Q703G9)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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).
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        POLS_IPNVS | Q703G9: 2pnl 3ide

(-) Related Entries Specified in the PDB File

2gef VP4 PROTEASE FROM ANOTHER BIRNAVIRUS (BLOTCHED SNAKEHEAD VIRUS, BSNV)
2pnl VP4 FROM IPNV IN THE SPACE GROUP P1 (ACYL-ENZYME)