1XCB

X-ray Structure of a Rex-Family Repressor/NADH Complex from Thermus Aquaticus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

X-Ray Structure of a Rex-Family Repressor/NADH Complex: Insights into the Mechanism of Redox Sensing

Sickmier, E.A.Brekasis, D.Paranawithana, S.Bonanno, J.B.Paget, M.S.Burley, S.K.Kielkopf, C.L.

(2005) Structure 13: 43-54

  • DOI: 10.1016/j.str.2004.10.012
  • Primary Citation of Related Structures:  
    1XCB

  • PubMed Abstract: 
  • The redox-sensing repressor Rex regulates transcription of respiratory genes in response to the intra cellular NADH/NAD(+) redox poise. As a step toward elucidating the molecular mechanism of NADH/NAD(+) sensing, the X-ray structure of Thermus aquaticus Rex (T-Rex) bound to effector NADH has been determined at 2 ...

    The redox-sensing repressor Rex regulates transcription of respiratory genes in response to the intra cellular NADH/NAD(+) redox poise. As a step toward elucidating the molecular mechanism of NADH/NAD(+) sensing, the X-ray structure of Thermus aquaticus Rex (T-Rex) bound to effector NADH has been determined at 2.9 A resolution. The fold of the C-terminal domain of T-Rex is characteristic of NAD(H)-dependent enzymes, whereas the N-terminal domain is similar to a winged helix DNA binding motif. T-Rex dimerization is primarily mediated by "domain-swapped" alpha helices. Each NADH molecule binds to the C-terminal domain near the dimer interface. In contrast to NAD(H)-dependent enzymes, the nicotinamide is deeply buried within a hydrophobic pocket that appears to preclude substrate entry. We show that T-Rex binds to the Rex operator, and NADH but not NAD(+) inhibits T-Rex/DNA binding activity. A mechanism for redox sensing by Rex family members is proposed by analogy with domain closure of NAD(H)-dependent enzymes.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Redox-sensing transcriptional repressor rexA, B, C, D, E, F, G211Thermus aquaticusMutation(s): 4 
Gene Names: rex
UniProt
Find proteins for Q9X2V5 (Thermus aquaticus)
Explore Q9X2V5 
Go to UniProtKB:  Q9X2V5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.232 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.24α = 90
b = 88.97β = 106.09
c = 112.91γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary