Crystal structure of the effector binding domain of a BenM variant (BenM R156H/T157S)

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Inducer responses of BenM, a LysR-type transcriptional regulator from Acinetobacter baylyi ADP1.

Craven, S.H.Ezezika, O.C.Haddad, S.Hall, R.A.Momany, C.Neidle, E.L.

(2009) Mol Microbiol 72: 881-894

  • DOI: https://doi.org/10.1111/j.1365-2958.2009.06686.x
  • Primary Citation of Related Structures:  
    2H99, 2H9B, 3GLB

  • PubMed Abstract: 

    BenM and CatM control transcription of a complex regulon for aromatic compound degradation. These Acinetobacter baylyi paralogues belong to the largest family of prokaryotic transcriptional regulators, the LysR-type proteins. Whereas BenM activates transcription synergistically in response to two effectors, benzoate and cis,cis-muconate, CatM responds only to cis,cis-muconate. Here, site-directed mutagenesis was used to determine the physiological significance of an unexpected benzoate-binding pocket in BenM discovered during structural studies. Residues in BenM were changed to match those of CatM in this hydrophobic pocket. Two BenM residues, R160 and Y293, were found to mediate the response to benzoate. Additionally, alteration of these residues caused benzoate to inhibit activation by cis,cis-muconate, positioned in a separate primary effector-binding site of BenM. The location of the primary site, in an interdomain cleft, is conserved in diverse LysR-type regulators. To improve understanding of this important family, additional regulatory mutants were analysed. The atomic-level structures were characterized of the effector-binding domains of variants that do not require inducers for activation, CatM(R156H) and BenM(R156H,T157S). These structures clearly resemble those of the wild-type proteins in their activated muconate-bound complexes. Amino acid replacements that enable activation without effectors reside at protein interfaces that may impact transcription through effects on oligomerization.

  • Organizational Affiliation

    Department of Microbiology, University of Georgia, Athens, GA 30602-2605, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HTH-type transcriptional regulator benM
A, B
312Acinetobacter baylyi ADP1Mutation(s): 2 
Gene Names: benMbenR
Find proteins for O68014 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1))
Explore O68014 
Go to UniProtKB:  O68014
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68014
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
H [auth B]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
O4 S
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
L [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.51α = 90
b = 66.587β = 90
c = 117.971γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description