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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SERINE PROTEASE DOMAIN OF SESBANIA MOSAIC VIRUS POLYPROTEIN
 
Authors :  P. Gayathri, P. S. Satheshkumar, K. Prasad, H. S. Savithri, M. R. N. Murt
Date :  10 Jun 05  (Deposition) - 25 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Viral Serine Protease Of Trypsin Fold, Beta-Barrel, Glutamyl Endopeptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Gayathri, P. S. Satheshkumar, K. Prasad, S. Nair, H. S. Savithri, M. R. N. Murthy
Crystal Structure Of The Serine Protease Domain Of Sesbania Mosaic Virus Polyprotein And Mutational Analysis Of Residue Forming The S1-Binding Pocket
Virology V. 346 440 2006
PubMed-ID: 16356524  |  Reference-DOI: 10.1016/J.VIROL.2005.11.011

(-) Compounds

Molecule 1 - SERINE PROTEASE
    Chains: A
    EC Number: 3.4.21.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PRSET-C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PROTEASE DOMAIN
    Gene: ORF2
    Organism Scientific: SESBANIA MOSAIC VIRUS
    Organism Taxid: 12558

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:181 , ALA A:280 , GLY A:282 , SER A:284 , HIS A:298BINDING SITE FOR RESIDUE GOL A 500

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:248 -A:277
2A:256 -A:256

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZYO)

(-) 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    
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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:184
 aligned with Q9EB08_9VIRU | Q9EB08 from UniProtKB/TrEMBL  Length:572

    Alignment length:186
                                   147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317      
         Q9EB08_9VIRU   138 SFYSPVKAGDEPASLVAIKSGPTTIGFGCRTKIDGEDCLLTAHHVWCNSMRPTGLAKAGKQVSVEDWEISMSSSDKMLDFAIVRVPTHVWSKLGVKSTPLVCPSSKDVITCYGGSSSDCLMSGVGSSSTSEFTWKLTHTCPTAAGWSGTPLYSSRGVVGMHVGFEEIGKLNRGVNMFYVANYLLRS 323
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------Peptidase_S39  -1zyoA01 A:158-314                                                                                                                            --------- Pfam domains
         Sec.struct. author ...eee........eeeeee..eeeeeeeee..--..eeeehhhhhh......eeee..eeee....eeeeee......eeeee.hhhhhhhhh............eeeeeeee.....eeeeeeeeee.....eeee...........eee....eeeeeeeeee...eeeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zyo A 138 SFYSPVKAGDEPASLVAIKSGPTTIGFGCRTKI--EDCLLTAHHVWCNSMRPTGLAKAGKQVSVEDWEISMSSSDKMLDFAIVRVPTHVWSKLGVKSTPLVCPSSKDVITCYGGSSSDCLMSGVGSSSTSEFTWKLTHTCPTAAGWSGTPLYSSRGVVGMHVGFEEIGKLNRGVNMFYVANYLLRS 323
                                   147       157       167  |  | 177       187       197       207       217       227       237       247       257       267       277       287       297       307       317      
                                                          170  |                                                                                                                                                      
                                                             173
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1ZYO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZYO)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_PA (797)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9EB08_9VIRU | Q9EB08)
molecular function
    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).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1lvm CATALYTICALLY ACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH PRODUCT
1q31 CRYSTAL STRUCTURE OF THE TOBACCO ETCH VIRUS PROTEASE C151A MUTANT