4KDD

Structure of Mycobacterium tuberculosis ribosome recycling factor in presence of detergent


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular flexibility of Mycobacterium tuberculosis ribosome recycling factor and its functional consequences: an exploration involving mutants.

Selvaraj, M.Govindan, A.Seshadri, A.Dubey, B.Varshney, U.Vijayan, M.

(2013) J Biosci 38: 845-855

  • DOI: 10.1007/s12038-013-9381-0
  • Primary Citation of Related Structures:  
    4KB4, 4KAW, 4KB2, 4KC6, 4KDD

  • PubMed Abstract: 
  • Internal mobility of the two domain molecule of ribosome recycling factor (RRF) is known to be important for its action. Mycobacterium tuberculosis RRF does not complement E. coli for its deficiency of RRF (in the presence of E. coli EF-G alone). Cry ...

    Internal mobility of the two domain molecule of ribosome recycling factor (RRF) is known to be important for its action. Mycobacterium tuberculosis RRF does not complement E. coli for its deficiency of RRF (in the presence of E. coli EF-G alone). Crystal structure had revealed higher rigidity of the M. tuberculosis RRF due to the presence of additional salt bridges between domains. Two inter-domain salt bridges and one between the linker region and the domain containing C-terminal residues were disrupted by appropriate mutations. Except for a C-terminal deletion mutant, all mutants showed RRF activity in E. coli when M. tuberculosis EF-G was also co-expressed. The crystal structures of the point mutants, that of the C-terminal deletion mutant and that of the protein grown in the presence of a detergent, were determined. The increased mobility resulting from the disruption of the salt bridge involving the hinge region allows the appropriate mutant to weakly complement E. coli for its deficiency of RRF even in the absence of simultaneous expression of the mycobacterial EF-G. The loss of activity of the C-terminal deletion mutant appears to be partly due to the rigidification of the molecule consequent to changes in the hinge region.


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome-recycling factorA185Mycobacterium tuberculosisMutation(s): 0 
Gene Names: frrMT2949MTCY274.13cRv2882c
Find proteins for P9WGY1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGY1 
Go to UniProtKB:  P9WGY1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMU
Query on DMU

Download CCD File 
A
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
CD
Query on CD

Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.37α = 90
b = 33.72β = 112.84
c = 61.51γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Database references