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(-) Description

Title :  CRYSTAL STRUCTURE OF TRANSMISSIBLE GASTROENTERITIS VIRUS PAPAIN-LIKE PROTEASE 1
 
Authors :  J. A. Wojdyla, I. Manolaridis, P. A. Tucker
Date :  24 Apr 10  (Deposition) - 08 Sep 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Papain-Like Protease, Tgev, Coronavirus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. Wojdyla, I. Manolaridis, P. B. Van Kasteren, M. Kikkert, E. J. Snijder, A. E. Gorbalenya, P. A. Tucker
Papain-Like Protease 1 From Transmissible Gastroenteritis Virus: Crystal Structure And Enzymatic Activity Toward Vira And Cellular Substrates.
J. Virol. V. 84 10063 2010
PubMed-ID: 20668092  |  Reference-DOI: 10.1128/JVI.00898-10

(-) Compounds

Molecule 1 - NON-STRUCTURAL PROTEIN 3
    ChainsA
    EC Number3.4.22.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM-11
    Expression System StrainROSETTA(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1071-1281
    Gene1A
    Organism CommonTGEV
    Organism ScientificPORCINE TRANSMISSIBLE GASTROENTERITIS CORONAVIRUS
    Organism Taxid11151
    StrainPURDUE
    SynonymPAPAIN-LIKE PROTEASE 1

 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
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:103 , CYS A:105 , CYS A:131 , CYS A:134BINDING SITE FOR RESIDUE ZN A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MP2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MP2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MP2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MP2)

(-) Exons   (0, 0)

(no "Exon" information available for 3MP2)

(-) 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:211
 aligned with R1A_CVPPU | P0C6V2 from UniProtKB/Swiss-Prot  Length:4017

    Alignment length:211
                                  1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280 
           R1A_CVPPU   1071 SLPPFKTTNLNGKIILKQGDNNCWINACCYQLQAFDFFNNEAWEKFKKGDVMDFVNLCYAATTLARGHSGDAEYLLELMLNDYSTAKIVLAAKCGCGEKEIVLERAVFKLTPLKESFNYGVCGDCMQVNTCRFLSVEGSGVFVHDILSKQTPEAMFVVKPVMHAVYTGTTQNGHYMVDDIEHGYCVDGMGIKPLKKRCYTSTLFINANVMT 1281
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Viral_protease-3mp2A01 A:10-220                                                                                                                                                                                     Pfam domains
         Sec.struct. author ......eeee..eeee.....hhhhhhhhhhhh......hhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhh....eeeeeeeee..eeeeeeeee.eee.......eeeee......eeeeeeeeeeeeeeeeeeee....hhhhh.....eeeeee......eeeeee....eeee..eee......eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mp2 A   10 SLPPFKTTNLNGKIILKQGDNNCWINACCYQLQAFDFFNNEAWEKFKKGDVMDFVNLCYAATTLARGHSGDAEYLLELMLNDYSTAKIVLAAKCGCGEKEIVLERAVFKLTPLKESFNYGVCGDCMQVNTCRFLSVEGSGVFVHDILSKQTPEAMFVVKPVMHAVYTGTTQNGHYMVDDIEHGYCVDGMGIKPLKKRCYTSTLFINANVMT  220
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219 

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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 3MP2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MP2)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (R1A_CVPPU | P0C6V2)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
    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: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:0008242    omega peptidase activity    Catalysis of the removal of terminal peptide residues that are substituted, cyclized or linked by isopeptide bonds (peptide linkages other than those of alpha-carboxyl to alpha-amino groups).
    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:0036459    thiol-dependent ubiquitinyl hydrolase activity    Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039520    induction by virus of host autophagy    Any process in which a virus activates or increases the frequency, rate or extent of autophagy in the host.
    GO:0039648    modulation by virus of host protein ubiquitination    Any process in which a virus modulates the frequency, rate or extent of protein ubiquitination in the host organism. Ubiquitination is the process in which one or more ubiquitin groups are added to a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0039548    suppression by virus of host IRF3 activity    Any process in which a virus stops, prevents, or reduces the activity of host IRF3 (interferon regulatory factor-3), a transcription factor in the RIG-I/MDA-5 signaling pathway. Viral infection triggers phosphorylation of cytoplasmic IRF3, which allows IRF3 to form a homodimer, migrate to the nucleus, and activate transcription of IFN-alpha and IFN-beta genes.
    GO:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
    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:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0044220    host cell perinuclear region of cytoplasm    The host cell cytoplasm situated near, or occurring around, the host nucleus.
    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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        R1A_CVPPU | P0C6V21lvo 1p9u 2amp 3zbd 4f49

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