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(-) Description

Title :  CRYSTAL STRUCTURE OF A NOVEL VIRAL PROTEASE WITH A SERINE/LYSINE CATALYTIC DYAD MECHANISM
 
Authors :  M. Paetzel, A. R. Feldman, J. Lee, B. Delmas
Date :  20 Mar 06  (Deposition) - 02 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (12x)
Biol. Unit 4:  A,B  (3x)
Biol. Unit 5:  A,B  (1x)
Keywords :  Birnavirus, Serine/Lysine Dyad Mechamism, Lysine General Base, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Feldman, J. Lee, B. Delmas, M. Paetzel
Crystal Structure Of A Novel Viral Protease With A Serine/Lysine Catalytic Dyad Mechanism
J. Mol. Biol. V. 358 1378 2006
PubMed-ID: 16584747  |  Reference-DOI: 10.1016/J.JMB.2006.02.045
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEASE VP4
    Chains: A, B
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: FRAGMENT OF VIRAL POLYPROTEIN (RESIDUES 558-773)
    Gene: BIRNAVIRIDAE
    Organism Scientific: BLOTCHED SNAKEHEAD VIRUS
    Organism Taxid: 311176

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (12x): AB
Biological Unit 4 (3x): AB
Biological Unit 5 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 96)
No.NameCountTypeFull Name
1MSE96Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 5 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2GEF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GEF)

(-) 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:198
 aligned with POLS_BSNV | Q8AZM0 from UniProtKB/Swiss-Prot  Length:1069

    Alignment length:211
                                   568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768 
            POLS_BSNV   559 DLPISLLQTLAYKQPLGRNSRIVHFTDGALFPVVAFGDNHSTSELYIAVRGDHRDLMSPDVRDSYALTGDDHKVWGATHHTYYVEGAPKKPLKFNVKTRTDLTILPVADVFWRADGSADVDVVWNDMPAVAGQSSSIALALASSLPFVPKAAYTGCLSGTNVQPVQFGNLKARAAHKIGLPLVGMTQDGGEDTRICTLDDAADHAFDSMES 769
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee....eeeeeeee...eeeeeeee....eeeeeeeeee..hhhhhhhhhhh.eee.....eee.ee.-------------.........eeeeeeeeeee.....eeeeeee.....ee...hhhhhhhhhhh......eee.eee..eee...hhhhhhhhhhh....eee........ee..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gef A 559 DLPISLLQTLAYKQPLGRNSRIVHFTDGALFPVVAFGDNHSTSELYIAVRGDHRDLmSPDVRDSYALTGDDHKVWGATH-------------KFNVKTRTDLTILPVADVFWRADGSADVDVVWNDmPAVAGQSSSIALALASSLPFVPKAAYTGCLSGTNVQPVQFGNLKARAAHKIGLPLVGmTQDGGEDTRICTLDDAADHAFDSmES 769
                                   568       578       588       598       608      |618       628        |-         -  |    658       668       678      |688       698       708       718       728       738    |  748       758       768 
                                                                                  615-MSE               637           651                               685-MSE                                                   743-MSE                 767-MSE


Chain B from PDB  Type:PROTEIN  Length:203
 aligned with POLS_BSNV | Q8AZM0 from UniProtKB/Swiss-Prot  Length:1069

    Alignment length:215
                                   568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768     
            POLS_BSNV   559 DLPISLLQTLAYKQPLGRNSRIVHFTDGALFPVVAFGDNHSTSELYIAVRGDHRDLMSPDVRDSYALTGDDHKVWGATHHTYYVEGAPKKPLKFNVKTRTDLTILPVADVFWRADGSADVDVVWNDMPAVAGQSSSIALALASSLPFVPKAAYTGCLSGTNVQPVQFGNLKARAAHKIGLPLVGMTQDGGEDTRICTLDDAADHAFDSMESTVTR 773
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee....eeeeeeee...eeeeeeee....eeeeeeeeee.......hhhhhh.eee.....eee....------------..........eeeeeeeeeee.....eeeeeee..........hhhhhhhhhhh......eee.eee..eee...hhhhhhhhhhhh...eee........ee..hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gef B 559 DLPISLLQTLAYKQPLGRNSRIVHFTDGALFPVVAFGDNHSTSELYIAVRGDHRDLmSPDVRDSYALTGDDHKVWGATH------------LKFNVKTRTDLTILPVADVFWRADGSADVDVVWNDmPAVAGQSSSIALALASSLPFVPKAAYTGCLSGTNVQPVQFGNLKARAAHKIGLPLVGmTQDGGEDTRICTLDDAADHAFDSmESTVTR 773
                                   568       578       588       598       608      |618       628        |-         - |     658       668       678      |688       698       708       718       728       738    |  748       758       768     
                                                                                  615-MSE               637          650                                685-MSE                                                   743-MSE                 767-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 2GEF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (POLS_BSNV | Q8AZM0)
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:0039621    T=13 icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=13 symmetry. The T=13 capsid is composed of 12 pentameric and 120 hexameric capsomeres.
    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.

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