2W24

M. tuberculosis Rv3291c complexed to Lysine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Ligand-Induced Structural Transitions, Mutational Analysis, and 'Open' Quaternary Structure of the M. Tuberculosis Feast/Famine Regulatory Protein (Rv3291C).

Shrivastava, T.Dey, A.Ramachandran, R.

(2009) J Mol Biol 392: 1007

  • DOI: https://doi.org/10.1016/j.jmb.2009.07.084
  • Primary Citation of Related Structures:  
    2W24, 2W25, 2W29

  • PubMed Abstract: 

    Rv3291c is a member of the feast/famine regulatory protein family that is known to form stable protein-DNA complexes. We report a specific oligomeric transition between hexadecameric and octameric/lower-order oligomers in the presence of Phe that supports an effector-mediated model for the disassembly of a nucleosome-like particle. We had generated two mutants, Gly102Thr and Glu104Ala, which are part of the essential 100-106 effector-binding loop. The Gly102Thr mutant adopts an unusual 'open' quaternary structure and offers interesting functional insights co-related to the binding of an effector. This is similar to the previously reported Escherichia coli Lrp co-crystallized in the presence of DNA where the interactions of the substrate with the N-terminal DNA binding domain presumably lead to symmetry deviations to the oligomeric association. The present structure represents a direct evidence to support that changes made to the effector-binding domain at the C-terminus also result in a functionally relevant quaternary structural change. Conversely, the Glu104Ala mutant retains the closed quaternary association observed in the native protein and reveals nonsymmetrical interaction effects in the two subunits of the dimer. We also report that the native protein unexpectedly binds Lys but does not recognize Arg and offer a structural explanation for it. Error-scaled difference distance matrix analysis suggests that the protein has a relatively flexible core that is presumably needed to mediate the structural changes necessary for the protein's regulatory functions.


  • Organizational Affiliation

    Molecular and Structural Biology Division, Central Drug Research Institute, P.O. Box 173, Chattar Manzil, Mahatma Gandhi Marg, Lucknow 226001, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
A, B
150Mycobacterium tuberculosisMutation(s): 0 
UniProt
Find proteins for P96896 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Explore P96896 
Go to UniProtKB:  P96896
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP96896
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LYS
Query on LYS

Download Ideal Coordinates CCD File 
C [auth A]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.98α = 90
b = 100.98β = 90
c = 99.311γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    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: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description