1TFO

Ribonuclease from Escherichia coli complexed with its inhibitor protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Relation between tRNase activity and the structure of colicin D according to X-ray crystallography

Yajima, S.Nakanishi, K.Takahashi, K.Ogawa, T.Hidaka, M.Kezuka, Y.Nonaka, T.Ohsawa, K.Masaki, H.

(2004) Biochem.Biophys.Res.Commun. 322: 966-973

  • DOI: 10.1016/j.bbrc.2004.07.206
  • Primary Citation of Related Structures:  
  • Also Cited By: 5ZNM

  • PubMed Abstract: 
  • Colicin D is a plasmid-encoded proteinaceous toxin which kills sensitive Escherichia coli. Toxicity stems from ribonuclease activity that targets exclusively four isoacceptors of tRNA(Arg) with a cleavage position between 38 and 39 of the correspondi ...

    Colicin D is a plasmid-encoded proteinaceous toxin which kills sensitive Escherichia coli. Toxicity stems from ribonuclease activity that targets exclusively four isoacceptors of tRNA(Arg) with a cleavage position between 38 and 39 of the corresponding anticodons. Since no other tRNAs with the same sequences at 38 and 39 as tRNA(Arg)s are cleaved, colicin D should be capable of recognizing some higher order structure of tRNAs. We report here two crystal structures of catalytic domains of colicin D which have different N-terminal lengths, both complexed with its cognate inhibitor protein, ImmD. A row of positive charge patches is found on the surface of the catalytic domain, suggestive of the binding site of the tRNAs. This finding, together with our refined tRNase activity experiments, indicates that the catalytic domain starting at position 595 has activity almost equivalent to that of colicin D.


    Organizational Affiliation

    Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan. yshun@nodai.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Colicin D
A
103Escherichia coliMutation(s): 0 
Gene Names: cda
Find proteins for P17998 (Escherichia coli)
Go to UniProtKB:  P17998
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Colicin D immunity protein
B
91Escherichia coliMutation(s): 0 
Gene Names: cdi
Find proteins for P11899 (Escherichia coli)
Go to UniProtKB:  P11899
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.258 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 56.171α = 90.00
b = 56.171β = 90.00
c = 149.307γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance