|PROSITE documentation PDOC00042|
The gntR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 60-70 residues present in transcriptional regulators of the gntR family. This family of bacterial regulators is named after Bacillus subtilis gntR, a repressor of the gluconate operon [1,2]. Six subfamilies have been described for the gntR family: fadR, hutC, plmA, mocR, ytrA, and araR, which regulate various biological processes and important bacterial metabolic pathways. The DNA-binding gntR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain a subfamily-specific effector-binding domain and/or an oligomerization domain. The fadR-like regulators, representing the largest subfamily, are involved in the regulation of oxidized substrates related to metabolic pathways or metabolism of amino acids. HutC-like proteins are involved in conjugative plasmid transfer in several Streptomyces species. PlmA is a cyanobacterial regulator of plasmid maintenance. The mocR subfamily encompasses proteins homologous to class I aminotransferase proteins, which bind pyridoxal phosphate as a cofactor. Most of the ytrA-like proteins take part in operons involved in ATP-binding cassette (ABC) transport systems. AraR is an autoregulatory protein with a C-terminal domain that binds a carbohydrate effector, similar to that present in regulators of the lacI/galR family (see <PDOC00366>) [3,4].
The crystal structures of fadR show that the N-terminal, DNA binding domain contains a small β-sheet (B) core and three α-helices (H) with a topology H1-B1-H2-H3-B2-B3 (see <PDB:1H9T>). Helices 2 and 3, connected via a tight turn, comprise the helix-turn-helix motif. The anti-parallel β-strands 2 and 3 together with B1 form a small β-sheet, which is called the wing. Helix 3 is termed the recognition helix as in most wHTHs it binds the DNA major groove. Here, only the N-terminal tip of the recognition helix makes specific DNA-contacts and the wing makes unusual sequence-specific contacts to the minor groove. Like other HTH proteins, most gntR-type regulators bind as homodimers to 2-fold symmetric DNA sequences in which each monomer recognizes half of the site [5,6].
Some proteins known to contain a gntR-type HTH domain:
The profile we developed covers the entire gntR-type HTH domain, from the well-conserved part of helix 1 to the end of the wing.Expert(s) to contact by email:
February 2004 / Text revised.
PROSITE method (with tools and information) covered by this documentation:
|1||Authors||Buck D. Guest J.R.|
|Title||Overexpression and site-directed mutagenesis of the succinyl-CoA synthetase of Escherichia coli and nucleotide sequence of a gene (g30) that is adjacent to the suc operon.|
|Source||Biochem. J. 260:737-747(1989).|
|2||Authors||Haydon D.J. Guest J.R.|
|Title||A new family of bacterial regulatory proteins.|
|Source||FEMS Microbiol. Lett. 63:291-295(1991).|
|3||Authors||Rigali S. Derouaux A. Giannotta F. Dusart J.|
|Title||Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies.|
|Source||J. Biol. Chem. 277:12507-12515(2002).|
|4||Authors||Lee M.H. Scherer M. Rigali S. Golden J.W.|
|Title||PlmA, a new member of the GntR family, has plasmid maintenance functions in Anabaena sp. strain PCC 7120.|
|Source||J. Bacteriol. 185:4315-4325(2003).|
|5||Authors||Van Aalten D.M.F. DiRusso C.C. Knudsen J.|
|Source||EMBO J. 20:2041-2050(2001).|
|6||Authors||Xu Y. Heath R.J. Li Z. Rock C.O. White S.W.|
|Title||The FadR.DNA complex. Transcriptional control of fatty acid metabolism in Escherichia coli.|
|Source||J. Biol. Chem. 276:17373-17379(2001).|