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(-) Description

Title :  CRYSTAL STRUCTURE OF YELLOWTAIL ASCITES VIRUS VP4 PROTEASE ACTIVE SITE MUTANT (K674A) REVEALS BOTH AN ACYL-ENZYME COMPLEX AND AN EMPTY ACTIVE SITE
 
Authors :  M. Paetzel, I. Y. W. Chung
Date :  30 Jan 13  (Deposition) - 27 Feb 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Viral Protease, Birnavirus, Serine-Lysine Dyad Mechanism, Alpha-Beta Protein Fold, Lysine General Base, Acyl-Enzyme, Product Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Y. Chung, M. Paetzel
Crystal Structures Of Yellowtail Ascites Virus Vp4 Protease Trapping An Internal Cleavage Site Trans Acyl-Enzyme Comple In A Native Ser/Lys Dyad Active Site.
J. Biol. Chem. V. 288 13068 2013
PubMed-ID: 23511637  |  Reference-DOI: 10.1074/JBC.M112.386953

(-) Compounds

Molecule 1 - YELLOWTAIL ASCITES VIRUS (YAV) VP4 PROTEASE
    Chains: A
    EC Number: 3.4.21.115
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B+
    Expression System Strain: TUNER (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: VIRAL PROTEIN 4 (VP4)
    Mutation: YES
    Organism Scientific: YELLOWTAIL ASCITES VIRUS
    Organism Taxid: 360000
    Strain: Y-6
 
Molecule 2 - YELLOWTAIL ASCITES VIRUS (YAV) VP4 PROTEASE
    Chains: B
    EC Number: 3.4.21.115
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B+
    Expression System Strain: TUNER (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: VIRAL PROTEIN 4 (VP4)
    Mutation: YES
    Organism Scientific: YELLOWTAIL ASCITES VIRUS
    Organism Taxid: 360000
    Strain: Y-6

 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  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BME-1Ligand/IonBETA-MERCAPTOETHANOL
2CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2CSO-1Mod. Amino AcidS-HYDROXYCYSTEINE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:668 , CSO A:669BINDING SITE FOR RESIDUE MG A 801
2AC2SOFTWAREGLU A:533 , PRO A:535 , CYS B:669 , HOH B:1069BINDING SITE FOR RESIDUE BME B 801
3AC3SOFTWAREHOH B:1037 , HOH B:1038 , HOH B:1039 , HOH B:1040 , HOH B:1073 , HOH B:1074BINDING SITE FOR RESIDUE MG B 802

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:588 -A:604
2B:588 -B:604

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4IZK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IZK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IZK)

(-) Exons   (0, 0)

(no "Exon" information available for 4IZK)

(-) 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:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh...eeeeeee......eeeeeeee.......eeeeeeeeee..hhhhhhhhhh.eee.....eeee............eeeeeeeeeee.....eeeeee.........hhhhhhhhhhh........ee..ee......ee...hhhhhhhhhhhh...eee......ee..hhhhhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4izk A 515 RFSRNLKDRLESNNYEEMELPPPTKGVIIPVVHTVESAPGEAFGSLLVIIPGAYPELLDPNQQVLSHFKNDTGCVWGIGEDIPFEGDDICYTALPLKEIKKNGNIVVEKVFAGPAMGPSCQLGLSLLVNDIDKGVPRMVFTGEIANDEETIVPIcGVDIAAIAAHEHGLPLVGCQPGVDEVVANTSLASHLIQSGALPVQKA 716
                                   524       534       544       554       564       574       584       594       604       614       624       634       644       654       664    |  674       684       694       704       714  
                                                                                                                                                                                    669-CSO                                           


Chain B from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhh..eeeeee......eeeeeeee......eeeeeeeeeee..hhhhhhhhhh.eee.....eeee............eeeeeeeeeee.....eeeee.....ee...hhhhhhhhhhh........ee..ee......ee...hhhhhhhhhhhh...eee......ee..hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4izk B 514 GRFSRNLKDRLESNNYEEMELPPPTKGVIIPVVHTVESAPGEAFGSLLVIIPGAYPELLDPNQQVLSHFKNDTGCVWGIGEDIPFEGDDICYTALPLKEIKKNGNIVVEKVFAGPAMGPSCQLGLSLLVNDIDKGVPRMVFTGEIANDEETIVPICGVDIAAIAAHEHGLPLVGCQPGVDEVVANTSLASHLIQSGALPVQKA 716
                                   523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713
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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 4IZK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IZK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IZK)

(-) Gene Ontology  (9, 9)

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 Related Entries

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        P89521_9VIRU | P89521: 4izj

(-) Related Entries Specified in the PDB File

2gef CRYSTAL STRUCTURE OF VP4 PROTEASE FROM BLOTCHED SNAKEHEAD VIRUS (BSNV)
2pnl CRYSTAL STRUCTURE OF VP4 PROTEASE FROM INFECTIOUS PANCREATIC NECROSIS VIRUS (IPNV) IN SPACE GROUP P1
2pnm CRYSTAL STRUCTURE OF VP4 PROTEASE FROM INFECTIOUS PANCREATIC NECROSIS VIRUS (IPNV) IN SPACE GROUP P6122
3p06 CRYSTAL STRUCTURE OF VP4 PROTEASE FROM TELLINA VIRUS 1 (TV- 1)
4izj