Letunic et al. (2017) Nucleic Acids Res doi: 10.1093/nar/gkx922
Letunic et al. (2020) Nucleic Acids Res doi: 10.1093/nar/gkaa937

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HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

SMART accession number:	SM00345
Description:	-
Interpro abstract (IPR000524):	Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon [ (PUBMED:2060763) ]. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined [ (PUBMED:11013219) ]. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus ( IPR011711 ). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies [ (PUBMED:11756427) ]. This entry represents the N-terminal DNA-binding domain of the GntR family.
GO process:	regulation of transcription, DNA-templated (GO:0006355)
GO function:	DNA-binding transcription factor activity (GO:0003700)
Family alignment:	View or CHROMA formatHMM/Web logoCLUSTALW formatMSF formatFASTA formatPIR format

There are 260179 HTH_GNTR domains in 257472 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Taxonomic distribution of proteins containing HTH_GNTR domain.

  This tree includes only several representative species. The complete taxonomic breakdown of all proteins with HTH_GNTR domain is also avaliable.

  Click on the protein counts, or double click on taxonomic names to display all proteins containing HTH_GNTR domain in the selected taxonomic class.

• Literature (relevant references for this domain)

• Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

  • Haydon DJ, Guest JR
  • A new family of bacterial regulatory proteins.
  • FEMS Microbiol Lett. 1991; 63: 291-5
  • Display abstract

  • A new family of bacterial regulatory proteins has been identified by sequence similarity. The family contains the repressor of the Bacillus subtilis gluconate operon (GntR), the regulators for histidine utilization in Pseudomonas putida (HutCPp) and Klebsiella aerogenes (HutCKa), the repressor (FadR) of fatty acid degradation in Escherichia coli, a regulator involved in the conjugal transfer of the broad host range plasmid pIJ101 (KorA), and three proteins of unidentified function in E. coli (GenA, P30 and PhnF). The proteins share amino acid sequence similarities in a 69-residue N-terminal region. A helix-turn-helix motif is predicted in the most highly-conserved segment of each protein suggesting that they are members of a new family of helix-turn-helix DNA-binding proteins.

  • Buck D, Guest JR
  • 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.
  • Biochem J. 1989; 260: 737-47
  • Display abstract

  • The succinyl-CoA synthetase of Escherichia coli is encoded by two genes, sucC (beta subunit) and sucD (alpha subunit), which are distal genes in the sucABCD operon. They are expressed from the suc promoter, which also expresses the dehydrogenase and dihydrolipoyl succinyl-transferase subunits of the 2-oxoglutarate dehydrogenase complex. Strategies have now been devised for the site-directed mutagenesis and independent expression of the succinyl-CoA synthetase (alpha 2 beta 2 tetramer) and the individual subunits. These involve (1) subcloning a promoterless sucCD fragment downstream of the lac promoter in M13mp10, and (2) precise splicing of the suc coding regions with the efficient atpE ribosome-binding site and expression from the thermoinducible lambda promoters in the pJLA503 vector. Succinyl-CoA synthetase specific activities were amplified 40-60-fold within 5 h of thermoinduction of the lambda promoters, and the alpha and beta subunits accounted for almost 30% of the protein in supernatant fractions of the cell-free extracts. Site-directed mutagenesis of potential CoA binding-site residues indicated that Trp-43 beta and His-50 beta are essential residues in the beta-subunit, whereas Cys-47 beta could be replaced by serine without inactivating the enzyme. No activity was detected after the histidine residue at the phosphorylation site of the alpha-subunit was replaced by aspartate (His-246 alpha----Asp), but this alteration seemed to have a deleterious effect on the accumulation of the enzyme in cell-free supernatant extracts. The nucleotide sequence of an unidentified gene (g30) that is adjacent to the sucABCD operon was defined by extending the sequence of the citric acid cycle gene cluster by 818 bp to 13379 bp: gltA-sdhCDAB-sucABCD-g30. This gene converges on the suc operon and encodes a product (P30) that contains 230 amino acids (Mr 27,251). Highly significant similarities were detected between the N-terminal region of P30 and those of GENA [the product of another unidentified gene (geneA) located upstream of the aceEF-lpd operon], and GNTR (a putative transcriptional repressor of the gluconate operon of Bacillus subtilis). Possible roles for GENA and P30 as transcriptional regulators of the adjacent operons encoding the pyruvate and 2-oxoglutarate dehydrogenase complexes are discussed.

• Metabolism (metabolic pathways involving proteins which contain this domain)

• Click the image to view the interactive version of the map in iPath

  % proteins involved KEGG pathway ID Description 8.57 map00252 Alanine and aspartate metabolism 8.57 map00300 Lysine biosynthesis 8.57 map00310 Lysine degradation 7.14 map00350 Tyrosine metabolism 7.14 map00400 Phenylalanine, tyrosine and tryptophan biosynthesis 7.14 map00360 Phenylalanine metabolism 7.14 map00401 Novobiocin biosynthesis 7.14 map00950 Alkaloid biosynthesis I 5.71 map00251 Glutamate metabolism 5.71 map00710 Carbon fixation 5.71 map00330 Arginine and proline metabolism 5.71 map00272 Cysteine metabolism 2.86 map00260 Glycine, serine and threonine metabolism 2.86 map00280 Valine, leucine and isoleucine degradation 2.86 map00620 Pyruvate metabolism 2.86 map00020 Citrate cycle (TCA cycle) 2.86 map00010 Glycolysis / Gluconeogenesis 1.43 map00271 Methionine metabolism This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with HTH_GNTR domain which could be assigned to a KEGG orthologous group, and not all proteins containing HTH_GNTR domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of HTH_GNTR domains in PDB

  PDB code	Main view	Title
  1e2x		FadR, fatty acid responsive transcription factor from E. coli
  1h9g		FadR, FATTY ACID RESPONSIVE TRANSCRIPTION FACTOR FROM E. COLI, in complex with myristoyl-CoA
  1h9t		FADR, FATTY ACID RESPONSIVE TRANSCRIPTION FACTOR FROM E. COLI IN COMPLEX WITH FADB OPERATOR
  1hw1		THE FADR-DNA COMPLEX: TRANSCRIPTIONAL CONTROL OF FATTY ACID METABOLISM IN ESCHERICHIA COLI
  1hw2		FADR-DNA COMPLEX: TRANSCRIPTIONAL CONTROL OF FATTY ACID METABOLISM IN ECHERICHIA COLI
  1v4r		Solution structure of Streptmycal repressor TraR
  2di3		Crystal structure of the transcriptional factor CGL2915 from Corynebacterium glutamicum
  2du9		crystal structure of the transcriptional factor from C.glutamicum
  2ek5		Crystal strucutre of the transcriptional factor from C.glutamicum at 2.2 angstrom resolution
  2hs5		Structural Genomics, the crystal structure of a putative transcriptional regulator GntR from Rhodococcus sp. RHA1
  2ra5		Crystal structure of the putative transcriptional regulator from Streptomyces coelicolor
  2wv0		Crystal structure of the GntR-HutC family member YvoA from Bacillus subtilis
  3bwg		The crystal structure of possible transcriptional regulator YydK from Bacillus subtilis subsp. subtilis str. 168
  3by6		Crystal structure of a transcriptional regulator from Oenococcus oeni
  3c7j		Crystal structure of transcriptional regulator (GntR family member) from Pseudomonas syringae pv. tomato str. DC3000
  3edp		The crystal structure of the protein lin2111 (functionally unknown) from Listeria innocua Clip11262
  3eet		Crystal structure of putative GntR-family transcriptional regulator
  3f8m		Crystal Structure of PhnF from Mycobacterium smegmatis
  3fms		Crystal structure of TM0439, a GntR transcriptional regulator
  3ic7		Crystal Structure of Putative Transcriptional Regulator of GntR Family from Bacteroides thetaiotaomicron
  3ihu		Crystal structure of DNA binding protein (YP_298823.1) from Ralstonia eutropha JMP134 at 1.92 A resolution
  3neu		The crystal structure of a functionally-unknown protein lin1836 from Listeria innocua Clip11262
  3sxy		Metal-free full-length structure of Tm0439, a metal-binding FCD family transcriptional regulator
  3tqn		Structure of the transcriptional regulator of the GntR family, from Coxiella burnetii.
  4egy		Crystal Structure of AraR(DBD) in complex with operator ORA1
  4egz		Crystal Structure of AraR(DBD) in complex with operator ORR3
  4h0e		Crystal Structure of mutant ORR3 in complex with NTD of AraR
  4ham		Crystal Structure of Transcriptional Antiterminator from Listeria monocytogenes EGD-e
  4mgr		The crystal structure of Bacillus subtilis GabR, an autorepressor and PLP- and GABA-dependent transcriptional activator of gabT
  4n0b		Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of GabT
  4p96		4P96
  4p9f		4P9F
  4p9u		4P9U
  4pdk		4PDK
  4r1h		4R1H
  4tv7		4TV7
  4u0v		4U0V
  4u0w		4U0W
  4u0y		4U0Y
  4wwc		4WWC
  4zs8		4ZS8
  5d4r		5D4R
  5d4s		5D4S
  5dv1		5DV1
  5dv5		5DV5
  5kvr		5KVR

• Links (links to other resources describing this domain)

• PROSITE	HTH_GNTR_FAMILY
  INTERPRO	IPR000524
  PFAM	gntR

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