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(-) Description

Title :  NMR STRUCTURE OF HEPATITIS C VIRUS NS3 SERINE PROTEASE COMPLEXED WITH THE NON-COVALENTLY BOUND PHENETHYLAMIDE INHIBITOR
 
Authors :  T. Eliseo, M. Gallo, M. Pennestri, R. Bazzo, D. O. Cicero
Date :  13 Mar 08  (Deposition) - 03 Feb 09  (Release) - 03 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Serine Protease, Ns3, Hepatitis C Virus, Non Covalent Inhibitor, Envelope Protein, Helicase, Hydrolase, Nucleotide-Binding, Rna Replication, Transmembrane, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Gallo, M. Pennestri, M. J. Bottomley, G. Barbato, T. Eliseo, M. Paci, F. Narjes, R. De Francesco, V. Summa, U. Koch, R. Bazzo, D. O. Cicero
Binding Of A Noncovalent Inhibitor Exploiting The S' Region Stabilizes The Hepatitis C Virus Ns3 Protease Conformation In The Absence Of Cofactor.
J. Mol. Biol. V. 385 1142 2009
PubMed-ID: 19061898  |  Reference-DOI: 10.1016/J.JMB.2008.11.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NS3 PROTEASE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System VariantDE3
    FragmentRESIDUES 1048-1206
    Organism ScientificHEPATITIS C VIRUS
    Organism Taxid11103
    Strain1B
 
Molecule 2 - PHENETHYLAMIDE
    ChainsB
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

NMR Structure (4, 4)
No.NameCountTypeFull Name
1FE31Mod. Amino Acid4-(2-AMINOETHYL)-3-CHLOROBENZOIC ACID
2IBU1Mod. Amino Acid2-METHYLPROPYL HYDROGEN CARBONATE
3OBF1Mod. Amino Acid(2S)-2-AMINO-4,4-DIFLUOROBUTANOIC ACID
4ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

NMR Structure (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:156 , ALA A:157 , CYS A:159 , LEU B:189BINDING SITE FOR RESIDUE IBU B 187
2AC2SOFTWARESER A:42 , SER A:133 , LEU A:135 , LYS A:136 , SER A:139 , PHE A:154BINDING SITE FOR RESIDUE OBF B 190
3AC3SOFTWARETHR A:38 , THR A:40 , GLN A:41 , SER A:42 , LYS A:136 , SER A:139 , GLU B:188BINDING SITE FOR RESIDUE FE3 B 191
4AC4SOFTWARECYS A:97 , THR A:98 , CYS A:99 , CYS A:145 , PRO A:146 , SER A:147BINDING SITE FOR RESIDUE ZN A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K1Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2K1Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2K1Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2K1Q)

(-) Exons   (0, 0)

(no "Exon" information available for 2K1Q)

(-) Sequences/Alignments

NMR Structure
   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:165
 aligned with P90191_9HEPC | P90191 from UniProtKB/TrEMBL  Length:3010

    Alignment length:192
                                  1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187      1197      1207      1217      1227      1237  
        P90191_9HEPC   1048 TGRDKNQVEGEVQVVSTATQSFLATCVNGVCWTVYHGAGSKTLAGPKGPITQMYTNVDQDLVGWQAPPGARSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPVSYLKGSSGGPLLCPSGHAVGIFRAAVCTRGVAKAVDFVPVESMETTMRSPVFTDNSSPPAVPQTFQVAHLHAPTGSGKSTK 1239
               SCOP domains d2k1qa_ A: automated matches                                                                                                                                                                     SCOP domains
               CATH domains 2k1qA01 A:22-94  [code=2.40.10.120, no name defined]                     2k1qA02 A:95-179 Trypsin-like serine proteases                                       ---------------------------------- CATH domains
               Pfam domains --------Peptidase_S29-2k1qA01 A:30-178                                                                                                                       ----------------------------------- Pfam domains
         Sec.struct. author ...........eeeee....eeeeeee..eeeee........ee....ee.eeeee....eeeee................eeeee.....eeeeee....eeeeeeeeehhhhh.....eeee...eeeeeeeeeee...eeeeeeeeehhhhhhhhh---------------------------hh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2k1q A   22 TGRDKNQVEGEVQVVSTATQSFLATCVNGVCWTVYHGAGSKTLAGPKGPITQMYTNVDQDLVGWQAPPGARSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPVSYLKGSSGGPLLCPSGHAVGIFRAAVCTRGVAKAVDFVPVESMETTMR---------------------------ASKKKK  186
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        |-         -         -      |184  
                                                                                                                                                                                        180                         181     

Chain B from PDB  Type:PROTEIN  Length:5
                                      
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                2k1q B  187 xELxx  191
                            |  ||
                            |  ||
                          187-IBU
                             190-OBF
                              191-FE3

   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  (1, 1)

NMR Structure

(-) CATH Domains  (2, 2)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (31, 31)

NMR Structure(hide GO term definitions)
Chain A   (P90191_9HEPC | P90191)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008026    ATP-dependent helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0017111    nucleoside-triphosphatase activity    Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
    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: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).
    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.
    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: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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0019087    transformation of host cell by virus    Any virus-induced change in the morphological, biochemical, or growth parameters of a cell.
    GO:0039694    viral RNA genome replication    The replication of a viral RNA genome.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    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:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    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: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.
    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:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        P90191_9HEPC | P901911dxw
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        P90191_9HEPC | P901913kee

(-) Related Entries Specified in the PDB File

1bt7 APO NS3 PROTEASE
1dwx COVALENT INHIBITOR - NS3 COMPLEX