2C06

NMR-based model of the complex of the toxin Kid and a 5-nucleotide substrate RNA fragment (AUACA)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: LOWEST 10 ENERGY STRUCTURES IN LOWEST ENERGY CLUSTER 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Model for RNA Binding and the Catalytic Site of the Rnase Kid of the Bacterial Pard Toxin-Antitoxin System.

Kamphuis, M.B.Bonvin, A.M.J.J.Monti, M.C.Lemonnier, M.Munoz-Gomez, A.Van Den Heuvel, R.H.H.Diaz-Orejas, R.Boelens, R.

(2006) J Mol Biol 357: 115

  • DOI: 10.1016/j.jmb.2005.12.033
  • Primary Citation of Related Structures:  
    2C06

  • PubMed Abstract: 
  • The toxin Kid and antitoxin Kis are encoded by the parD operon of Escherichia coli plasmid R1. Kid and its chromosomal homologues MazF and ChpBK have been shown to inhibit protein synthesis in cell extracts and to act as ribosome-independent endoribonucleases in vitro ...

    The toxin Kid and antitoxin Kis are encoded by the parD operon of Escherichia coli plasmid R1. Kid and its chromosomal homologues MazF and ChpBK have been shown to inhibit protein synthesis in cell extracts and to act as ribosome-independent endoribonucleases in vitro. Kid cleaves RNA preferentially at the 5' side of the A residue in the nucleotide sequence 5'-UA(A/C)-3' of single-stranded regions. Here, we show that RNA cleavage by Kid yields two fragments with a 2':3'-cyclic phosphate group and a free 5'-OH group, respectively. The cleavage mechanism is similar to that of RNases A and T1, involving the uracil 2'-OH group. Via NMR titration studies with an uncleavable RNA mimic, we demonstrate that residues of both monomers of the Kid dimer together form a concatenated RNA-binding surface. Docking calculations based on the NMR chemical shifts, the cleavage mechanism and previously reported mutagenesis data provide a detailed picture of the position of the AUACA fragment within the binding pocket. We propose that residues D75, R73 and H17 form the active site of the Kid toxin, where D75 and R73 are the catalytic base and acid, respectively. The RNA sequence specificity is defined by residues T46, S47, A55, F57, T69, V71 and R73. Our data show the importance of these residues for Kid function, and the implications of our results for related toxins, such as MazF, CcdB and RelE, are discussed.


    Organizational Affiliation

    Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
KID TOXIN PROTEINA, B110Escherichia coliMutation(s): 0 
Gene Names: pemK
EC: 3.1
UniProt
Find proteins for P13976 (Escherichia coli)
Explore P13976 
Go to UniProtKB:  P13976
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13976
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*AP*UP*AP*CP*AP)-3'C5N/A
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: LOWEST 10 ENERGY STRUCTURES IN LOWEST ENERGY CLUSTER 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-01-15
    Changes: Data collection, Other