Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.13 kDa 
• Atom Count: 4119 
• Modelled Residue Count: 432 
• Deposited Residue Count: 624 
• Unique protein chains: 1

2H99

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

• DOI: 10.2210/pdb2H99/pdb

• Classification: TRANSCRIPTION
• Organism(s): Acinetobacter baylyi ADP1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-06-09 Released: 2007-06-26 
• Deposition Author(s): Ezezika, O.C., Craven, S.H., Neidle, E.L., Momany, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.204 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Literature

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

• PubMed: 19400783 
• DOI: 10.1111/j.1365-2958.2009.06686.x
• Primary Citation of Related Structures:  
  3GLB, 2H99, 2H9B


• 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.

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Related Citations: 

• Distinct Effector-binding Sites Enable Synergistic Transcriptional Activation By BenM, a LysR-type Regulator
  Ezezika, O.C., Haddad, S., Clark, T.J., Neidle, E.L., Momany, C.
  () To be published --: --

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator benM	A, B	312	Acinetobacter baylyi ADP1	Mutation(s): 2  Gene Names: benM, benR, ACIAD1435
UniProt
Find proteins for O68014 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore O68014  Go to UniProtKB:  O68014

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A], F [auth A], G [auth A], K [auth B], L [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.204 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.937	α = 90
b = 66.506	β = 90
c = 117.495	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-06-09 
• Released Date: 2007-06-26 
Deposition Author(s): Ezezika, O.C., Craven, S.H., Neidle, E.L., Momany, C.

Revision History  

• 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