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(-) Description

Title :  C-TERMINAL MUTANT (W550N) OF HCV/J4 RNA POLYMERASE
 
Authors :  J. Jaeger, A. Cherry, C. Dennis
Date :  13 Dec 14  (Deposition) - 31 Dec 14  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hepatitis C Virus, Replication, Function Analysis, Viral Rna Polymerase, Rdrp, Rna Rntp Mg, Nucleotide Transfer, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Cherry, C. A. Dennis, A. Baron, L. E. Eisele, P. A. Thommes, J. Jaeger
Hydrophobic And Charged Residues In The C-Terminal Arm Of Hepatitis C Virus Rna-Dependent Rna Polymerase Regulate Initiation And Elongation.
J. Virol. V. 89 2052 2015
PubMed-ID: 25428878  |  Reference-DOI: 10.1128/JVI.01106-14

(-) Compounds

Molecule 1 - HCV J4 RNA POLYMERASE (NS5B)
    Chains: A, B
    EC Number: 2.7.7.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET23A
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2420-2989
    Gene: NS5B
    Mutation: YES
    Organism Common: HCV
    Organism Scientific: HEPATITIS C VIRUS ISOLATE HC-J4
    Organism Taxid: 420174
    Synonym: RNA-DEPENDENT RNA POLYMERASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION
2UTP2Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:220 , ASP A:318 , ASP A:319 , UTP A:1003BINDING SITE FOR RESIDUE MN A 1001
2AC2SOFTWAREASP A:220 , THR A:221 , ASP A:318 , UTP A:1003BINDING SITE FOR RESIDUE MN A 1002
3AC3SOFTWARELYS A:141 , ARG A:158 , LEU A:159 , ILE A:160 , ASP A:220 , THR A:221 , ARG A:222 , CYS A:223 , PHE A:224 , ASP A:225 , SER A:282 , THR A:287 , ASN A:291 , ASP A:318 , ASP A:319 , SER A:556 , MN A:1001 , MN A:1002 , HOH A:1209 , HOH A:1221 , HOH A:1270 , HOH A:1306BINDING SITE FOR RESIDUE UTP A 1003
4AC4SOFTWAREASP B:220 , ASP B:318 , ASP B:319 , UTP B:1003 , HOH B:1188BINDING SITE FOR RESIDUE MN B 1001
5AC5SOFTWAREASP B:220 , THR B:221 , ASP B:318 , UTP B:1003BINDING SITE FOR RESIDUE MN B 1002
6AC6SOFTWARELYS B:141 , ARG B:158 , LEU B:159 , ILE B:160 , ASP B:220 , THR B:221 , ARG B:222 , CYS B:223 , PHE B:224 , ASP B:225 , SER B:282 , ASP B:318 , ASP B:319 , SER B:556 , GLY B:557 , MN B:1001 , MN B:1002 , HOH B:1165 , HOH B:1183 , HOH B:1188 , HOH B:1211 , HOH B:1255BINDING SITE FOR RESIDUE UTP B 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RY5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RY5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RY5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RY5)

(-) Exons   (0, 0)

(no "Exon" information available for 4RY5)

(-) 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:565
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.................hhhhhh...hhh.eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee...eee............eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhhh....eeeeeee.....eeeeeee.hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ry5 A   1 SMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKATAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWRHRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSGNFVAGYSGGDIYHSLS 565
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560     


Chain B from PDB  Type:PROTEIN  Length:565
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.................hhhhhh...hhh.eee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.......hhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee...eee............eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............hhhh.ee..eeeeeee.....eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ry5 B   1 SMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGYGAKDVRNLSSRAVNHIRSVWEDLLEDTETPIDTTIMAKSEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIYQCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKATAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFTLHSYSPGEINRVASCLRKLGVPPLRTWRHRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSGNFVAGYSGGDIYHSLS 565
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560
   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 4RY5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RY5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RY5)

(-) Gene Ontology  (79, 79)

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 Related Entries

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UniProtKB/Swiss-Prot
        POLG_HCVJ4 | O92972: 1nb4 1nb6 1nb7 2f55 2mts 2xhu 2xhv 2xhw 2yoj 3cso 3gnv 3gnw 3gol 3hky 3lkh 3mwv 3mww 3ska 3ske 3skh 3tyq 3tyv 3u4o 3u4r 3uph 3upi 4dru 4eaw 4gmc 4iz0 4j02 4j04 4j06 4j08 4j0a 4jjs 4jju 4jtw 4jty 4jtz 4ju1 4ju2 4ju3 4ju4 4ju6 4ju7 4jvq 4jy0 4jy1 4mz4 4oow 4ry4 4ry6 4ry7 5czb 5nph

(-) Related Entries Specified in the PDB File

1nb4 4ry4 4ry6 4ry7