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(-) Description

Title :  2.75 ANGSTROM STRUCTURE OF THE D347G D348G MUTANT STRUCTURE OF SAPPORO VIRUS RDRP POLYMERASE
 
Authors :  S. Fullerton, I. Robel, L. Schuldt, J. Gebhardt, P. Tucker, J. Rohayem
Date :  07 Mar 07  (Deposition) - 01 May 07  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.76
Chains :  Asym./Biol. Unit :  A
Keywords :  Nucleotide-Binding, Nucleotidyltransferase, Covalent Protein-Rna Linkage, Rna Elongation, Transferase Activity, Capsid Protein, Rna Replication, Structural Protein, Protease, Helicase, Hydrolase, Transferase, Rna-Directed Rna Polymerase, Polyprotein, Atp-Binding, Thiol Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Fullerton, I. Robel, L. Schuldt, J. Gebhardt, P. Tucker, J. Rohayem
The 2. 76 Angstrom Resolution Structure Of The D347G D348G Mutant Structure Of Sapporo Virus Rdrp Polymerase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RNA-DIRECTED RNA POLYMERASE
    ChainsA
    EC Number2.7.7.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET M11
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentRNA POLYMERASE, RESIDUES 1135-1649
    MutationYES
    Organism ScientificSAPPORO VIRUS
    Organism Taxid95342
    Other DetailsFROM DRESDEN CALICI-LABORATORY
    StrainSAPPORO
    SynonymSAPOVIRUS RNA-DEPENDANT RNA-POLYMERASE
    TissueINTESTINE
    VariantDRESDEN ISOLATE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2UUW)

(-) Sites  (0, 0)

(no "Site" information available for 2UUW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:210 -Pro A:211

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RDRP_SSRNA_POSPS50507 RdRp of positive ssRNA viruses catalytic domain profile.POLG_SVM931370-1495  1A:236-361

(-) Exons   (0, 0)

(no "Exon" information available for 2UUW)

(-) 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:490
 aligned with POLG_SVM93 | Q69014 from UniProtKB/Swiss-Prot  Length:2208

    Alignment length:497
                                  1144      1154      1164      1174      1184      1194      1204      1214      1224      1234      1244      1254      1264      1274      1284      1294      1304      1314      1324      1334      1344      1354      1364      1374      1384      1394      1404      1414      1424      1434      1444      1454      1464      1474      1484      1494      1504      1514      1524      1534      1544      1554      1564      1574      1584      1594      1604      1614      1624       
          POLG_SVM93   1135 DEFQWKGLPVVKSGLDVGGMPTGTRYHRSPAWPEEQPGETHAPAPFGSGDKRYTFSQTEMLVNGLKPYTEPTAGVPPQLLSRAVTHVRSYIETIIGTHRSPVLTYHQACELLERTTSCGPFVQGLKGDYWDEEQQQYTGVLANHLEQAWDKANKGIAPRNAYKLALKDELRPIEKNKAGKRRLLWGCDAATTLIATAAFKAVATRLQVVTPMTPVAVGINMDSVQMQVMNDSLKGGVLYCLDYSKWDSTQNPAVTAASLAILERFAEPHPIVSCAIEALSSPAEGYVNDIKFVTRGGLPSGMPFTSVVNSINHMIYVAAAILQAYESHNVPYTGNVFQVETIHTYGDDCMYSVCPATASIFHTVLANLTSYGLKPTAADKSDAIKPTNTPVFLKRTFTQTPHGIRALLDITSITRQFYWLKANRTSDPSSPPAFDRQARSAQLENALAYASQHGPVMFDTVRQIAIKTAQGEGLVLVNTNYDQALATYNAWFIGGTV 1631
               SCOP domains d2uuwa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------RdRP_1-2uuwA01 A:19-490                                                                                                                                                                                                                                                                                                                                                                                                                                                                 ------- Pfam domains
         Sec.struct. author ..eee..eeeee...........eeeee............eee............hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh..............hhh.ee....eehhhhhhhhhhhhhhhhh......eeeeee...eeehhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..eeee..eeee..........hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhheeeee..eeeeeehhhhhhhhhhhhhhhhhh.....-------.......ee..eeee......eeeehhhhhhhhhheeeeeee.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RDRP_SSRNA_POS  PDB: A:236-361 UniProt: 1370-1495                                                                             ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2uuw A    1 DEFQWKGLPVVKSGLDVGGMPTGTRYHRSPAWPEEQPGETHAPAPFGSGDKRYTFSQTEMLVNGLKPYTEPTAGVPPQLLSRAVTHVRSYIETIIGTHRSPVLTYHQACELLERTTSCGPFVQGLKGDYWDEEQQQYTGVLANHLEQAWDKANKGIAPRNAYKLALKDELRPIEKNKAGKRRLLWGCDAATTLIATAAFKAVATRLQVVTPMTPVAVGINMDSVQMQVMNDSLKGGVLYCLDYSKWDSTQNPAVTAASLAILERFAEPHPIVSCAIEALSSPAEGYVNDIKFVTRGGLPSGMPFTSVVNSINHMIYVAAAILQAYESHNVPYTGNVFQVETIHTYGGGCMYSVCPATASIFHTVLANLTSYGLKPT-------IKPTNTPVFLKRTFTQTPHGIRALLDITSITRQFYWLKANRTSDPSSPPAFDRQARSAQLENALAYASQHGPVMFDTVRQIAIKTAQGEGLVLVNTNYDQALATYNAWFIGGTV  497
                                    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     |   -   |   390       400       410       420       430       440       450       460       470       480       490       
                                                                                                                                                                                                                                                                                                                                                                                                                 376     384                                                                                                                 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2UUW)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: RdRP (210)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (POLG_SVM93 | Q69014)
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: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: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:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    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:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    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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    Thr A:210 - Pro A:211   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_SVM93 | Q690142ckw 2uut 2wk4

(-) Related Entries Specified in the PDB File

2ckw THE 2.3 A RESOLUTION STRUCTURE OF THE SAPPORO VIRUS RNA DEPENDANT RNA POLYMERASE.
2uut THE 2.4 ANGSTROM RESOLUTION STRUCTURE OF THE D346G MUTANT OF THE SAPPORO VIRUS RDRP POLYMERASE