3LSP

Crystal Structure of DesT bound to desCB promoter and oleoyl-CoA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

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Literature

Structural basis for the transcriptional regulation of membrane lipid homeostasis.

Miller, D.J., Zhang, Y.M., Subramanian, C., Rock, C.O., White, S.W.

(2010) Nat Struct Mol Biol 17: 971-975

  • DOI: https://doi.org/10.1038/nsmb.1847
  • Primary Citation of Related Structures:  
    3LSJ, 3LSP, 3LSR

  • PubMed Abstract: 

    DesT is a transcriptional repressor that regulates the genes that control the unsaturated:saturated fatty acid ratio available for membrane lipid synthesis. DesT bound to unsaturated acyl-CoA has a high affinity for its cognate palindromic DNA-binding site, whereas DesT bound to saturated acyl-CoA does not bind this site. Structural analyses of the DesT-oleoyl-CoA-DNA and DesT-palmitoyl-CoA complexes reveal that acyl chain shape directly influences the packing of hydrophobic core residues within the DesT ligand-binding domain. These changes are propagated to the paired DNA-binding domains via conformational changes to modulate DNA binding. These structural interpretations are supported by the in vitro and in vivo characterization of site-directed mutants. The regulation of DesT by the unsaturated:saturated ratio of acyl chains rather than the concentration of a single ligand is a paradigm for understanding transcriptional regulation of membrane lipid homeostasis.

    • Organizational Affiliation: 

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DesT220Pseudomonas aeruginosaMutation(s): 1 
Gene Names: desT, PA4890
UniProt
Find proteins for Q9HUS3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HUS3 
Go to UniProtKB:  Q9HUS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HUS3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*AP*CP*AP*TP*CP*AP*GP*TP*GP*AP*AP*CP*GP*CP*TP*TP*GP*TP*TP*GP*AP*CP*TP*CP*GP*AP*TP*TP*G)-3')31N/A
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*AP*AP*TP*CP*GP*AP*GP*TP*CP*AP*AP*CP*AP*AP*GP*CP*GP*TP*TP*CP*AP*CP*TP*GP*AP*TP*GP*TP*A)-3')C [auth D]31N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.385α = 90
b = 78.385β = 90
c = 147.988γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-02-21
    Changes: Data collection