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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: Last update:February 2004 / Text revised.
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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). | |
PubMed ID | 2548486 |
2 | Authors | Haydon D.J. Guest J.R. |
Title | A new family of bacterial regulatory proteins. | |
Source | FEMS Microbiol. Lett. 63:291-295(1991). | |
PubMed ID | 2060763 |
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). | |
PubMed ID | 11756427 | |
DOI | 10.1074/jbc.M110968200 |
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). | |
PubMed ID | 12867439 |
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). | |
PubMed ID | 11279025 | |
DOI | 10.1074/jbc.M100195200 |