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(-) Description

Title :  NMR SOLUTION STRUCTURE OF THE NUCLEASE DOMAIN FROM THE REPLICATOR INITIATOR PROTEIN FROM PORCINE CIRCOVIRUS PCV2
 
Authors :  S. Vega-Rocha, I. L. Byeon, B. Gronenborn, A. M. Gronenborn, R. Campos- Olivas
Date :  31 Jul 06  (Deposition) - 12 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (31x)
Keywords :  Alpha+Beta, Hydrolase, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Vega-Rocha, I. L. Byeon, B. Gronenborn, A. M. Gronenborn, R. Campos-Olivas
Solution Structure, Divalent Metal And Dna Binding Of The Endonuclease Domain From The Replication Initiation Protein From Porcine Circovirus 2
J. Mol. Biol. V. 367 473 2007
PubMed-ID: 17275023  |  Reference-DOI: 10.1016/J.JMB.2007.01.002
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REPLICASE
    ChainsA
    EC Number3.1.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3A
    Expression System StrainROSSETA (DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 2-116 OF REP PCV2
    GeneREP, ORF1
    Organism ScientificPORCINE CIRCOVIRUS 2
    Organism Taxid85708

 Structural Features

(-) Chains, Units

  
NMR Structure (31x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2HW0)

(-) Sites  (0, 0)

(no "Site" information available for 2HW0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HW0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HW0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HW0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HW0)

(-) Exons   (0, 0)

(no "Exon" information available for 2HW0)

(-) 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:115
 aligned with O93192_PCV2 | O93192 from UniProtKB/TrEMBL  Length:314

    Alignment length:115
                                    11        21        31        41        51        61        71        81        91       101       111     
          O93192_PCV2     2 PSKKNGRSGPQPHKRWVFTLNNPSEDERKKIRDLPISLFDYFIVGEEGNEEGRTPHLQGFANFVKKQTFNKVKWYLGARCHIEKAKGTDQQNKEYCSKEGNLLMECGAPRSQGQR 116
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeee..hhhhhhhhhh.hhh.eeeeeeeee........eeeeeeee....hhhhhhhhhh...eee....hhhhhhhhhhh...eeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2hw0 A   2 PSKKNGRSGPQPHKRWVFTLNNPSEDERKKIRDLPISLFDYFIVGEEGNEEGRTPHLQGFANFVKKQTFNKVKWYLGARCHIEKAKGTDQQNKEYCSKEGNLLMECGAPRSQGQR 116
                                    11        21        31        41        51        61        71        81        91       101       111     

Chain A from PDB  Type:PROTEIN  Length:115
 aligned with REP_PCV2 | Q8BB16 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:115
                                    11        21        31        41        51        61        71        81        91       101       111     
             REP_PCV2     2 PSKKNGRSGPQPHKRWVFTLNNPSEDERKKIREPPISLFDYFIVGEEGNEEGRTPHLQGFANFVKKQTFNKVKWYLGARCHIEKAKGTDQQNKEYCSKEGNLLIECGAPRSQGQR 116
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeee..hhhhhhhhhh.hhh.eeeeeeeee........eeeeeeee....hhhhhhhhhh...eee....hhhhhhhhhhh...eeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2hw0 A   2 PSKKNGRSGPQPHKRWVFTLNNPSEDERKKIRDLPISLFDYFIVGEEGNEEGRTPHLQGFANFVKKQTFNKVKWYLGARCHIEKAKGTDQQNKEYCSKEGNLLMECGAPRSQGQR 116
                                    11        21        31        41        51        61        71        81        91       101       111     

   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 2HW0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HW0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HW0)

(-) Gene Ontology  (22, 29)

NMR Structure(hide GO term definitions)
Chain A   (REP_PCV2 | Q8BB16)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0042624    ATPase activity, uncoupled    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction is not directly coupled to any other reaction.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016888    endodeoxyribonuclease activity, producing 5'-phosphomonoesters    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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: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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0018142    protein-DNA covalent cross-linking    The formation of a covalent cross-link between DNA and a protein.
    GO:0039684    rolling circle single-stranded viral DNA replication    A rolling circle viral DNA replication that begins with a single-stranded viral DNA genome.
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.

Chain A   (O93192_PCV2 | O93192)
molecular function
    GO:0042624    ATPase activity, uncoupled    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction is not directly coupled to any other reaction.
    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:0016888    endodeoxyribonuclease activity, producing 5'-phosphomonoesters    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
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:0018142    protein-DNA covalent cross-linking    The formation of a covalent cross-link between DNA and a protein.

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6928 ASSIGNMENT OF RESONANCES