2B3T

Structure of complex between E. coli translation termination factor RF1 and the PrmC methyltransferase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Molecular basis for bacterial class I release factor methylation by PrmC

Graille, M., Heurgue-Hamard, V., Champ, S., Mora, L., Scrima, N., Ulryck, N., van Tilbeurgh, H., Buckingham, R.H.

(2005) Mol Cell 20: 917-927

  • DOI: 10.1016/j.molcel.2005.10.025
  • Primary Citation of Related Structures:  
    2B3T

  • PubMed Abstract: 

    • Class I release factors bind to ribosomes in response to stop codons and trigger peptidyl-tRNA hydrolysis at the P site. Prokaryotic and eukaryotic RFs share one motif: a GGQ tripeptide positioned in a loop at the end of a stem region that interacts with the ribosomal peptidyl transferase center ...

    Class I release factors bind to ribosomes in response to stop codons and trigger peptidyl-tRNA hydrolysis at the P site. Prokaryotic and eukaryotic RFs share one motif: a GGQ tripeptide positioned in a loop at the end of a stem region that interacts with the ribosomal peptidyl transferase center. The glutamine side chain of this motif is specifically methylated in both prokaryotes and eukaryotes. Methylation in E. coli is due to PrmC and results in strong stimulation of peptide chain release. We have solved the crystal structure of the complex between E. coli RF1 and PrmC bound to the methyl donor product AdoHCy. Both the GGQ domain (domain 3) and the central region (domains 2 and 4) of RF1 interact with PrmC. Structural and mutagenic data indicate a compact conformation of RF1 that is unlike its conformation when it is bound to the ribosome but is similar to the crystal structure of the protein alone.

    Organizational Affiliation: 

    Institut de Biochimie et Biophysique Moléculaire et Cellulaire, CNRS, UMR8619, Université Paris-Sud, Orsay, France.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein methyltransferase hemKA276Escherichia coliMutation(s): 0 
Gene Names: hemK
EC: 2.1.1 (PDB Primary Data), 2.1.1.297 (UniProt)
Find proteins for P0ACC1 (Escherichia coli (strain K12))
Explore P0ACC1 
Go to UniProtKB:  P0ACC1
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide chain release factor 1B360Escherichia coliMutation(s): 0 
Gene Names: prfA, sueB, uar
Find proteins for P0A7I0 (Escherichia coli (strain K12))
Explore P0A7I0 
Go to UniProtKB:  P0A7I0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH
Download Ideal Coordinates CCD File 
 C [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.244 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.54α = 90
b = 77.47β = 90
c = 89.49γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XSCALEdata scaling
MOLREPphasing
CNSrefinement
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2018-02-14
    Changes: Structure summary