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(-) Description

Title :  NMR-BASED MODEL OF THE COMPLEX OF THE TOXIN KID AND A 5-NUCLEOTIDE SUBSTRATE RNA FRAGMENT (AUACA)
 
Authors :  M. B. Kamphuis, A. M. J. J. Bonvin, M. C. Monti, M. Lemonnier, A. Munoz-Gomez, R. H. H. Van Den Heuvel, R. Diaz-Orejas, R. Boelens
Date :  25 Aug 05  (Deposition) - 08 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (10x)
Keywords :  Docking, Dna Replication, Mazf, Plasmid Maintenance, Post Segregational Killing, Protein-Rna Complex, Ribonuclease, Rna Cleavage, Rnase, Toxin-Antitoxin, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. B. Kamphuis, A. M. J. J. Bonvin, M. C. Monti, M. Lemonnier, A. Munoz-Gomez, R. H. H. Van Den Heuvel, R. Diaz-Orejas, R. Boelens
Model For Rna Binding And The Catalytic Site Of The Rnase Kid Of The Bacterial Pard Toxin- Antitoxin System.
J. Mol. Biol. V. 357 115 2006
PubMed-ID: 16413033  |  Reference-DOI: 10.1016/J.JMB.2005.12.033

(-) Compounds

Molecule 1 - KID TOXIN PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidR1
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymPROTEIN PEMK
 
Molecule 2 - 5'-R(*AP*UP*AP*CP*AP)-3'
    ChainsC
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (10x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2C06)

(-) Sites  (0, 0)

(no "Site" information available for 2C06)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C06)

(-) Cis Peptide Bonds  (2, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10Asp A:12 -Pro A:13
21, 2, 3, 4, 5, 6, 7, 8, 9, 10Asp B:12 -Pro B:13

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C06)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C06)

(-) Exons   (0, 0)

(no "Exon" information available for 2C06)

(-) 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:110
 aligned with PEMK_ECOLX | P13976 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:110
                                    33        43        53        63        73        83        93       103       113       123       133
           PEMK_ECOLX    24 MERGEIWLVSLDPTAGHEQQGTRPVLIVTPAAFNRVTRLPVVVPVTSGGNFARTAGFAVSLDGVGIRTTGVVRCDQPRTIDMKARGGKRLERVPETIMNEVLGRLSTILT 133
               SCOP domains d2c06a1 A:1-110 Kid toxin protein (ParD)                                                                       SCOP domains
               CATH domains 2c06A00 A:1-110  [code=2.30.30.110, no name defined]                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...........eeeeee..hhhhhhhhh..eeeeee...........eee..........eee....ee.hhhhhh.eeeee.hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2c06 A   1 MERGEIWLVSLDPTAGHEQQGTRPVLIVTPAAFNRVTRLPVVVPVTSGGNFARTAGFAVSLDGVGIRTTGVVRCDQPRTIDMKARGGKRLERVPETIMNEVLGRLSTILT 110
                                    10        20        30        40        50        60        70        80        90       100       110

Chain B from PDB  Type:PROTEIN  Length:110
 aligned with PEMK_ECOLX | P13976 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:110
                                    33        43        53        63        73        83        93       103       113       123       133
           PEMK_ECOLX    24 MERGEIWLVSLDPTAGHEQQGTRPVLIVTPAAFNRVTRLPVVVPVTSGGNFARTAGFAVSLDGVGIRTTGVVRCDQPRTIDMKARGGKRLERVPETIMNEVLGRLSTILT 133
               SCOP domains d2c06b1 B:1-110 Kid toxin protein (ParD)                                                                       SCOP domains
               CATH domains 2c06B00 B:1-110  [code=2.30.30.110, no name defined]                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...........eeeeee..hhhhhhhhh..eeeeee...........eee..........eee....ee........eeeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2c06 B   1 MERGEIWLVSLDPTAGHEQQGTRPVLIVTPAAFNRVTRLPVVVPVTSGGNFARTAGFAVSLDGVGIRTTGVVRCDQPRTIDMKARGGKRLERVPETIMNEVLGRLSTILT 110
                                    10        20        30        40        50        60        70        80        90       100       110

Chain C from PDB  Type:RNA  Length:5
                                     
                 2c06 C   1 AUACA   5

   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  (1, 2)

NMR Structure

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C06)

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A,B   (PEMK_ECOLX | P13976)
molecular function
    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:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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  Sites
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  Cis Peptide Bonds
    Asp A:12 - Pro A:13   [ RasMol ]  
    Asp B:12 - Pro B:13   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PEMK_ECOLX | P139761m1f

(-) Related Entries Specified in the PDB File

1m1f KID TOXIN PROTEIN FROM E.COLI PLASMID R1