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(-) Description

Title :  1.65A RESOLUTION STRUCTURE OF NORWALK VIRUS PROTEASE CONTAINING A COVALENTLY BOUND DIPEPTIDYL INHIBITOR
 
Authors :  S. Lovell, K. P. Battaile, Y. Kim, K. C. Tiew, S. R. Mandadapu, K. R. Allis W. C. Groutas, K. O. Chang
Date :  21 Nov 11  (Deposition) - 05 Sep 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Protease, Norovirus, Norwalk Virus, Antiviral Inhibitors, Dipeptidyl Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kim, S. Lovell, K. C. Tiew, S. R. Mandadapu, K. R. Alliston, K. P. Battaile, W. C. Groutas, K. O. Chang
Broad-Spectrum Antivirals Against 3C Or 3C-Like Proteases O Picornaviruses, Noroviruses, And Coronaviruses.
J. Virol. V. 86 11754 2012
PubMed-ID: 22915796  |  Reference-DOI: 10.1128/JVI.01348-12

(-) Compounds

Molecule 1 - 3C-LIKE PROTEASE
    ChainsA, B
    EC Number3.4.22.66
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1101-1281
    GeneORF1
    Organism ScientificNOROVIRUS
    Organism Taxid524364
    StrainGI/HUMAN/UNITED STATES/NORWALK/1968
    Synonym3CLPRO

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2K362Ligand/Ion(1S,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)-1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1-SULFONIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2K361Ligand/Ion(1S,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)-1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1-SULFONIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2K361Ligand/Ion(1S,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)-1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1-SULFONIC ACID
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2K362Ligand/Ion(1S,2S)-2-({N-[(BENZYLOXY)CARBONYL]-L-LEUCYL}AMINO)-1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPANE-1-SULFONIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:7 , LYS A:88 , CL B:201BINDING SITE FOR RESIDUE CL A 201
2AC2SOFTWAREPRO A:78 , ARG A:147 , ARG B:108BINDING SITE FOR RESIDUE CL A 202
3AC3SOFTWAREHIS A:30 , GLN A:110 , ARG A:112 , THR A:134 , CYS A:139 , HIS A:157 , ALA A:158 , ALA A:159 , ALA A:160 , HOH A:317 , HOH A:376BINDING SITE FOR RESIDUE K36 A 203
4AC4SOFTWARECL A:201 , SER B:7 , LYS B:88BINDING SITE FOR RESIDUE CL B 201
5AC5SOFTWARETHR B:4 , ARG B:8BINDING SITE FOR RESIDUE CL B 202
6AC6SOFTWAREHIS B:30 , GLN B:110 , THR B:134 , CYS B:139 , HIS B:157 , ALA B:158 , ALA B:159 , ALA B:160 , HOH B:320 , HOH B:380 , HOH B:381 , HOH B:382BINDING SITE FOR RESIDUE K36 B 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UR9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UR9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UR9)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NV_3CL_PROPS51537 Norovirus 3C-like protease (NV 3CLpro) domain profile.POLG_NVN681101-1281
 
  2A:1-173
B:1-173
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NV_3CL_PROPS51537 Norovirus 3C-like protease (NV 3CLpro) domain profile.POLG_NVN681101-1281
 
  1A:1-173
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NV_3CL_PROPS51537 Norovirus 3C-like protease (NV 3CLpro) domain profile.POLG_NVN681101-1281
 
  1-
B:1-173
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NV_3CL_PROPS51537 Norovirus 3C-like protease (NV 3CLpro) domain profile.POLG_NVN681101-1281
 
  2A:1-173
B:1-173

(-) Exons   (0, 0)

(no "Exon" information available for 3UR9)

(-) Sequences/Alignments

Asymmetric 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:164
 aligned with POLG_NVN68 | Q83883 from UniProtKB/Swiss-Prot  Length:1789

    Alignment length:175
                                  1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228      1238      1248      1258      1268     
          POLG_NVN68   1099 FEAPPTLWSRVTKFGSGWGFWVSPTVFITTTHVVPTGVKEFFGEPLSSIAIHQAGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCSVLIKRDSGELLPLAVRMGAIASMRIQGRLVHGQSGMLLTGANAKGMDLGTIPGDCGAPYVHKRGNDWVVCGVHAAATKSGNTVVCAVQA 1273
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhheeee..eeeee....eeeee.hhh.....ee..ee...eeeeee..eeeeee...........ee........eeeeeee.....eeeeeeeeeeeeeeee..eeeeeeeeee.----------.........eeeeee..eeeeeeeeeee...-.eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --NV_3CL_PRO  PDB: A:1-173 UniProt: 1101-1281                                                                                                                                   PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ur9 A   -1 HMAPPTLWSRVTKFGSGWGFWVSPTVFITTTHVVPTGVKEFFGEPLSSIAIHQAGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCSVLIKRDSGELLPLAVRMGAIASMRIQGRLVHGQSGMLL----------GTIPGDCGAPYVHKRGNDWVVCGVHAAATKS-NTVVCAVQA  173
                                     8        18        28        38        48        58        68        78        88        98       108       118   |     -    |  138       148       158    | |168     
                                                                                                                                                     122        133                           163 |        
                                                                                                                                                                                                165        

Chain B from PDB  Type:PROTEIN  Length:165
 aligned with POLG_NVN68 | Q83883 from UniProtKB/Swiss-Prot  Length:1789

    Alignment length:174
                                  1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269    
          POLG_NVN68   1100 EAPPTLWSRVTKFGSGWGFWVSPTVFITTTHVVPTGVKEFFGEPLSSIAIHQAGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCSVLIKRDSGELLPLAVRMGAIASMRIQGRLVHGQSGMLLTGANAKGMDLGTIPGDCGAPYVHKRGNDWVVCGVHAAATKSGNTVVCAVQA 1273
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh.eeee..eeeee....eeeee.hhh.....ee..ee...eeeeee..eeeeee...........ee........eeeeeee.....eeeeeeeeeeeeeeee..eeeeeeeeee.---------..........eeeeee..eeeeeeeeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -NV_3CL_PRO  PDB: B:1-173 UniProt: 1101-1281                                                                                                                                   PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3ur9 B    0 MAPPTLWSRVTKFGSGWGFWVSPTVFITTTHVVPTGVKEFFGEPLSSIAIHQAGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCSVLIKRDSGELLPLAVRMGAIASMRIQGRLVHGQSGMLL---------LGTIPGDCGAPYVHKRGNDWVVCGVHAAATKSGNTVVCAVQA  173
                                     9        19        29        39        49        59        69        79        89        99       109       119  |      -  |    139       149       159       169    
                                                                                                                                                    122       132                                         

   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  (0, 0)

(no "SCOP Domain" information available for 3UR9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UR9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UR9)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (POLG_NVN68 | Q83883)
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:0003724    RNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a RNA helix.
    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: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: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: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:0044419    interspecies interaction between organisms    Any process in which an organism has an effect on an organism of a different species.
    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.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_NVN68 | Q838832fyq 2fyr 2lnc 3ur6 4imq 4imz 4in1 4in2 4inh 4xbb 4xbc 4xbd 5dg6 5dgj 5e0g 5e0h 5e0j 5t6d 5t6f 5t6g 5tg1 5tg2

(-) Related Entries Specified in the PDB File

3ur6 4dcd 4f49