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(-) Description

Title :  STRUCTURE OF THE AUTOCATALYTIC CYSTEINE PROTEASE DOMAIN OF POTYVIRUS HELPER-COMPONENT PROTEINASE
 
Authors :  K. Ye
Date :  22 Apr 11  (Deposition) - 04 May 11  (Release) - 04 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (4x)
Keywords :  Cysteine Protease, Proteolysis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Guo, J. Lin, K. Ye
Structure Of The Autocatalytic Cysteine Protease Domain Of Potyvirus Helper-Component Proteinase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HELPER COMPONENT PROTEINASE
    ChainsA
    EC Number3.4.22.45
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A-SMT3
    Expression System StrainROSETTA(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCYSTEINE PROTEASE DOMAIN
    GeneHC-PRO
    Organism ScientificTURNIP MOSAIC VIRUS
    Organism Taxid12230
    StrainJAPANESE
    SynonymHC-PRO

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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(-) Sites  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HC_PRO_CPDPS51744 Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain profile.POLG_TUMVJ698-820  1A:336-458
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HC_PRO_CPDPS51744 Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain profile.POLG_TUMVJ698-820  1A:336-458
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HC_PRO_CPDPS51744 Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain profile.POLG_TUMVJ698-820  4A:336-458

(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:123
 aligned with POLG_TUMVJ | P89509 from UniProtKB/Swiss-Prot  Length:3164

    Alignment length:123
                                   707       717       727       737       747       757       767       777       787       797       807       817   
           POLG_TUMVJ   698 MYIAKEGYCYINIFLAMLVNVKESQAKEFTKVVRDKLVGELGKWPTLLDVATACYFLKVFYPDVANAELPRMLVDHKTKIIHVVDSYGSLSTGYHVLKTNTVEQLIKFTRCNLESSLKHYRVG 820
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Peptidase_C6-3rnvA01 A:336-458                                                                                              Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeeee....eeeee................hhhhhhhhhhh...hhhhhhee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HC_PRO_CPD  PDB: A:336-458 UniProt: 698-820                                                                                 PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rnv A 336 MYIAKEGYCYINIFLAMLVNVKESQAKEFTKVVRDKLVGELGKWPTLLDVATACYFLKVFYPDVANAELPRMLVDHKTKIIHVVDSYGSLSTGYHVLKTNTVEQLIKFTRCNLESSLKHYRVG 458
                                   345       355       365       375       385       395       405       415       425       435       445       455   

   Legend:   → Mismatch (orange background)
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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 3RNV)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A   (POLG_TUMVJ | P89509)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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:0016818    hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides    Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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: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.
    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.
biological process
    GO:0018144    RNA-protein covalent cross-linking    The formation of a covalent cross-link between RNA and a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0039694    viral RNA genome replication    The replication of a viral RNA genome.
cellular component
    GO:0019029    helical viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles; the subunits are arranged to form a protein helix with the genetic material contained within. Tobacco mosaic virus has such a capsid structure.
    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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