Crystal structure of the transcriptional factor from C.glutamicum at 2.2 angstrom resolution

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.225 

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The structures of transcription factor CGL2947 from Corynebacterium glutamicum in two crystal forms: A novel homodimer assembling and the implication for effector-binding mode

Gao, Y.G.Yao, M.Itou, H.Zhou, Y.Tanaka, I.

(2007) Protein Sci 16: 1878-1886

  • DOI: https://doi.org/10.1110/ps.072976907
  • Primary Citation of Related Structures:  
    2DU9, 2EK5

  • PubMed Abstract: 

    Among the transcription factors, the helix-turn-helix (HTH) GntR family comprised of FadR, HutC, MocR, YtrA, AraR, and PlmA subfamilies regulates the most varied biological processes. Generally, proteins belonging to this family contain an N-terminal DNA-binding domain and a C-terminal effector-binding/oligomerization domain. The members of the YtrA subfamily are much shorter than other members of this family, with chain lengths of 120-130 residues with about 50 residues located in the C-terminal domain. Because of this length, the mode of dimerization and the ability to bind effectors by the C-terminal domain are puzzling. Here, we first report the structure of the transcription factor CGL2947 from Corynebacterium glutamicum, which belongs to the YtrA family. The monomer is composed of a DNA-binding domain containing a winged HTH motif in the N terminus and two helices (alpha4 and alpha5) with a fishhook-shaped arrangement in the C terminus. Helices alpha4 and alpha5 of two monomers intertwine together to form a novel homodimer assembly. The effector-accommodating pocket with 2-methyl-2,4-pentanediol (MPD) docked was located, and it was suggested to represent a novel mode of effector binding. The structures in two crystal forms (MPD-free and -bound in the proposed effector-binding pocket) were solved. The structural variations have implications regarding how the effector-induced conformational change modulates DNA affinity for YtrA family members.

  • Organizational Affiliation

    Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Predicted transcriptional regulators
A, B, C, D
129Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: Cgl2947
Find proteins for Q8NLJ5 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
Explore Q8NLJ5 
Go to UniProtKB:  Q8NLJ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NLJ5
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.225 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.638α = 90
b = 74.494β = 90
c = 182.152γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2020-09-09
    Changes: Data collection, Database references, Derived calculations, Structure summary