title: The structures of transcription factor CGL2947 from Corynebacterium glutamicum in two crystal forms: a novel homodimer assembling and the implication for effector-binding mode.
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.
authors.affiliation: Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.
authors.forename: Yong-Gui
authors.initials: YG
authors.lastname: Gao
authors.forename: Min
authors.initials: M
authors.lastname: Yao
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Itou
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhou
authors.forename: Isao
authors.initials: I
authors.lastname: Tanaka
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D048230:Corynebacterium glutamicum / Q000235:genetics*; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D019281:Dimerization; D006018:Glycols / Q000378:metabolism; D019077:Helix-Turn-Helix Motifs; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013059:Spectrum Analysis, Raman; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D014867:Water / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D006018:Glycols; D011994:Recombinant Proteins; D014157:Transcription Factors; D014867:Water; C011480:hexylene glycol