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(-) Description

Title :  STRUCTURE-BASED ANALYSIS OF THE INTERACTION BETWEEN THE SIMIAN VIRUS 40 T-ANTIGEN ORIGIN BINDING DOMAIN AND SINGLE-STRANDED DNA
 
Authors :  G. Meinke, P. A. Bullock, A. Bohm
Date :  31 Jan 11  (Deposition) - 23 Feb 11  (Release) - 23 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym./Biol. Unit :  A
Keywords :  Origin Binding Domain, Dna Replication, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Meinke, P. J. Phelan, A. Fradet-Turcotte, A. Bohm, J. Archambault, P. A. Bullock
Structure-Based Analysis Of The Interaction Between The Simian Virus 40 T-Antigen Origin Binding Domain And Single-Stranded Dna.
J. Virol. V. 85 818 2011
PubMed-ID: 20980496  |  Reference-DOI: 10.1128/JVI.01738-10

(-) Compounds

Molecule 1 - LARGE T ANTIGEN
    ChainsA
    EC Number3.6.4.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-4T
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentORIGIN BINDING DOMAIN
    Organism CommonSV40
    Organism ScientificSIMIAN VIRUS 40
    Organism Taxid10633
    SynonymLT, LT-AG

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CME1Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2SCN1Ligand/IonTHIOCYANATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:228 , GLU A:229 , TYR A:230 , LEU A:231BINDING SITE FOR RESIDUE SCN A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QK2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:239 -Pro A:240

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QK2)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1T_AG_OBDPS51287 Large T-antigen (T-ag) origin-binding domain (OBD) profile.LT_SV40139-254  1A:139-254

(-) Exons   (0, 0)

(no "Exon" information available for 3QK2)

(-) 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    
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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:132
 aligned with LT_SV40 | P03070 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:133
                                   138       148       158       168       178       188       198       208       218       228       238       248       258   
              LT_SV40   129 KRKVEDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISRHNSYNHNILFFLTPHRHRVSAINNYAQKLCTFSFLICKGVNKEYLMYSALTRDPFSVIEESLPGGLKEHDFNPEE 261
               SCOP domains d3qk2a_ A: The origin  DNA-binding domain of SV40 T-antigen                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------T_Ag_DNA_bind- 3qk2A01 A:136-229                                                              -------------------------------- Pfam domains
         Sec.struct. author hhhhhh....hhhhhhhh...-.....eeeeeeeeehhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeeeeehhhhhhhhhhhhh....eeeee..hhhhhhhhh....eeeeee......hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------T_AG_OBD  PDB: A:139-254 UniProt: 139-254                                                                           ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qk2 A 129 GSKVEDPKDFPSELLSFLSHA-FSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISRHNSYNHNILFFLTPHRHRVSAINNYAQKLcTFSFLICKGVNKEYLMYSALTRDPFSVIEESLPGGLKEHDFNPES 261
                                   138       148| |    158       168       178       188       198       208       218       228       238       248       258   
                                              149 |                                                              216-CME                                         
                                                151                                                                                                              

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QK2)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Rep (10)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LT_SV40 | P03070)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003688    DNA replication origin binding    Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    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: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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
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:0006268    DNA unwinding involved in DNA replication    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.
    GO:0039686    bidirectional double-stranded viral DNA replication    A viral DNA replication process where replication occurs in both directions from the starting point. This creates two replication forks, moving in opposite directions.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039645    modulation by virus of host G1/S transition checkpoint    Any viral process that modulates the frequency, rate or extent of the host cell G1/S transition checkpoint.
    GO:0060153    modulation by virus of host cell cycle    Any viral process that modulates the rate or extent of progression through the cell cycle.
    GO:0039648    modulation by virus of host protein ubiquitination    Any process in which a virus modulates the frequency, rate or extent of protein ubiquitination in the host organism. Ubiquitination is the process in which one or more ubiquitin groups are added to a protein.
    GO:0039649    modulation by virus of host ubiquitin-protein ligase activity    The process in which a virus effects a change in host ubiquitin-protein ligase activity. Ubiquitin-protein ligase activity catalyzes the reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0039576    suppression by virus of host JAK1 activity    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host JAK1 (Janus Kinase 1) activity. In the host, binding of a ligand to a receptor triggers activation of JAK proteins, which phosphorylate tyrosine residues on the receptor creating sites for STAT proteins to bind, which are in turn phosphorylated and activated by JAK proteins. By blocking JAK1 activity, many viruses block the host signal transduction pathway.
    GO:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    GO:0039502    suppression by virus of host type I interferon-mediated signaling pathway    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0039693    viral DNA genome replication    The replication of a viral DNA 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:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LT_SV40 | P030701ejl 1gh6 1n25 1q1s 1q1t 1svl 1svm 1svo 1tbd 1z1d 2fuf 2h1l 2if9 2ipr 2itj 2itl 2nl8 2ntc 2tbd 3qn2 4e2i 4fgn 4gdf 4rxh 5d9i 5tct

(-) Related Entries Specified in the PDB File

2fuf THE SAME PROTEIN IN A HEXAMERIC SPACE GROUP
2if9 THE SAME PROTEIN AS A CYS216-CYS216 DISULFIDE-LINKED DIMER
2itl THE SAME PROTEIN COMPLEXED TO DOUBLE STRANDED DNA
2ntc THE SAME PROTEIN COMPLEXED TO DOUBLE STRANDED DNA