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(-) Description

Title :  THE CRYSTAL STRUCTURE OF PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME VIRUS (PRRSV) LEADER PROTEASE NSP1
 
Authors :  Y. Sun, F. Xue, Y. Guo, M. Ma, Z. Lou, Z. Rao
Date :  26 Jul 09  (Deposition) - 27 Oct 09  (Release) - 27 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Prrsv, Nsp1, Zinc Finger, Papain-Like Cysteine Protease, Crystal Structure, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Sun, F. Xue, Y. Guo, M. Ma, N. Hao, X. C. Zhang, Z. Lou, X. Li, Z. Rao
Crystal Structure Of Porcine Reproductive And Respiratory Syndrome Virus Leader Protease Nsp1Alpha
J. Virol. V. 83 10931 2009
PubMed-ID: 19706710  |  Reference-DOI: 10.1128/JVI.02579-08
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NON-STRUCTURAL PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: LEADER PROTEASE NSP1, RESIDUES 1-180
    Gene: ORF1A
    Organism Common: PRRSV
    Organism Scientific: PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME VIRUS
    Organism Taxid: 28344

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:70 , CYS A:76 , HIS A:146 , MET A:180BINDING SITE FOR RESIDUE ZN A 181
2AC2SOFTWARECYS A:8 , CYS A:10 , CYS A:25 , CYS A:28BINDING SITE FOR RESIDUE ZN A 182

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IFU)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:71 -Pro A:72

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:175
 aligned with B6VGX5_PRRSV | B6VGX5 from UniProtKB/TrEMBL  Length:2473

    Alignment length:175
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175     
         B6VGX5_PRRSV     6 DRCTCTPNARVFVAEGQVYCTRCLSARSLLPLNLQVPELGVLGLFYRPEEPLRWTLPRAFPTVECSPAGACWLSAIFPIARMTSGNLNFQQRMVRVAAEIYRAGQLTPTVLKTLQVYERGCRWYPIVGPVPGVGVYANSLHVSDKPFPGATHVLTNLPLPQRPKPEDFCPFECAM 180
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee....eee...............hhhhhhhhhh........................hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhh.......eeee.........eee....ee........eeee.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ifu A   6 DRCTCTPNARVFVAEGQVYCTRCLSARSLLPLNLQVPELGVLGLFYRPEEPLRWTLPRAFPTVECSPAGACWLSAIFPIARMTSGNLNFQQRMVRVAAEIYRAGQLTPTVLKTLQVYERGCRWYPIVGPVPGVGVYANSLHVSDKPFPGATHVLTNLPLPQRPKPEDFCPFECAM 180
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175
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  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 3IFU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IFU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IFU)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (B6VGX5_PRRSV | B6VGX5)
molecular function
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    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: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: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.
    GO:0019082    viral protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
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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