4IHT

Crystal Structure of BenM_DBD/benA site 1 DNA Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N11-A sequence motif by LysR-type transcriptional regulators.

Alanazi, A.M.Neidle, E.L.Momany, C.

(2013) Acta Crystallogr.,Sect.D 69: 1995-2007

  • DOI: 10.1107/S0907444913017320
  • Primary Citation of Related Structures:  4IHS

  • PubMed Abstract: 
  • LysR-type transcriptional regulators (LTTRs) play critical roles in metabolism and constitute the largest family of bacterial regulators. To understand protein-DNA interactions, atomic structures of the DNA-binding domain and linker-helix regions of ...

    LysR-type transcriptional regulators (LTTRs) play critical roles in metabolism and constitute the largest family of bacterial regulators. To understand protein-DNA interactions, atomic structures of the DNA-binding domain and linker-helix regions of a prototypical LTTR, BenM, were determined by X-ray crystallography. BenM structures with and without bound DNA reveal a set of highly conserved amino acids that interact directly with DNA bases. At the N-terminal end of the recognition helix (α3) of a winged-helix-turn-helix DNA-binding motif, several residues create hydrophobic pockets (Pro30, Pro31 and Ser33). These pockets interact with the methyl groups of two thymines in the DNA-recognition motif and its complementary strand, T-N11-A. This motif usually includes some dyad symmetry, as exemplified by a sequence that binds two subunits of a BenM tetramer (ATAC-N7-GTAT). Gln29 forms hydrogen bonds to adenine in the first position of the recognition half-site (ATAC). Another hydrophobic pocket defined by Ala28, Pro30 and Pro31 interacts with the methyl group of thymine, complementary to the base at the third position of the half-site. Arg34 interacts with the complementary base of the 3' position. Arg53, in the wing, provides AT-tract recognition in the minor groove. For DNA recognition, LTTRs use highly conserved interactions between amino acids and nucleotide bases as well as numerous less-conserved secondary interactions.


    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.
      (2007) J.Mol.Biol. 367(3): 616
    • 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(4): 881
    • Oligomerization of BenM, a LysR-type transcriptional regulator: structural basis for the aggregation of proteins in this family.r
      Ezezika, O.C.,Haddad, S.,Neidle, E.L.,Momany, C.
      (2007) Acta Crystallogr.,Sect.F 63(Pt 5): 361


    Organizational Affiliation

    Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HTH-type transcriptional regulator BenM
A, B, C, D
94Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)Gene Names: benM (benR)
Find proteins for O68014 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1))
Go to UniProtKB:  O68014
Entity ID: 2
MoleculeChainsLengthOrganism
benA site 1 DNAE,G25N/A
Entity ID: 3
MoleculeChainsLengthOrganism
benA site 1 DNA - complementF,H25N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.956α = 90.00
b = 300.295β = 90.00
c = 46.003γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-10-02
    Type: Database references
  • Version 1.2: 2014-01-15
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description