HTH_XRE

Helix-turn-helix XRE-family like proteins

• SMART accession number: SM00530
• Interpro abstract (IPR001387):

  This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).

• GO function: sequence-specific DNA binding (GO:0043565)

There are 9313 HTH_XRE domains in 9188 proteins in SMART's nrdb database.

Literature (relevant references for this domain)

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

• Wood HE, Devine KM, McConnell DJ
• Characterisation of a repressor gene (xre) and a temperature-sensitive allele from the Bacillus subtilis prophage, PBSX.
• Gene. 1990; 96: 83-8

The defective prophage of Bacillus subtilis 168, PBSX, is a chromosomally based element which encodes a non-infectious phage-like particle with bactericidal activity. PBSX is induced by agents which elicit the SOS response. In a PBSX thermoinducible strain which carries the xhi1479 mutation, PBSX is induced by raising the growth temperature from 37 degrees C to 48 degrees C. A 1.2-kb fragment has been cloned which complements the xhi1479 mutation. The nucleotide sequence of this fragment contains an open reading frame (ORF) which encodes a protein of 113 amino acids (aa). This aa sequence resembles that of other bacteriophage repressors and suggests that the N-terminal region forms a helix-turn-helix motif, typical of the DNA-binding domain of many bacterial regulatory proteins. The ORF is preceded by four 15-bp direct repeats, each of which contains an internal palindromic sequence, and by sequences resembling a SigA-dependent promoter. The nt sequence of an equivalent fragment from the PBSX thermoinducible strain has also been determined. There are three aa differences within the ORF compared to the wild type, one of which lies within the helix-turn-helix segment. This ORF encodes a repressor protein of PBSX.

• Mondragon A, Subbiah S, Almo SC, Drottar M, Harrison SC
• Structure of the amino-terminal domain of phage 434 repressor at 2.0 A resolution.
• J Mol Biol. 1989; 205: 189-200

The crystal structure of the amino-terminal domain of phage 434 repressor has been solved using molecular replacement methods and refined to an R-factor of 19.3% against data to 2.0 A resolution. The protein comprises five short alpha-helices. Two of these form a helix-turn-helix motif, very similar to those found in related proteins. The protein is remarkably similar to the Cro protein from the same phage.

Metabolism (metabolic pathways involving proteins which contain this domain)

% proteins involved	KEGG pathway ID	Description
25.00	map00760	Nicotinate and nicotinamide metabolism
17.50	map00400	Phenylalanine, tyrosine and tryptophan biosynthesis
5.00	map00251	Glutamate metabolism
5.00	map00230	Purine metabolism
3.75	map00350	Tyrosine metabolism
3.75	map00910	Nitrogen metabolism
3.75	map00252	Alanine and aspartate metabolism
3.75	map00530	Aminosugars metabolism
3.75	map00360	Phenylalanine metabolism
3.75	map00401	Novobiocin biosynthesis
3.75	map00710	Carbon fixation
3.75	map00330	Arginine and proline metabolism
3.75	map00950	Alkaloid biosynthesis I
3.75	map00272	Cysteine metabolism
1.25	map03020	RNA polymerase
1.25	map00562	Inositol phosphate metabolism
1.25	map00903	Limonene and pinene degradation
1.25	map00240	Pyrimidine metabolism
1.25	map00361	gamma-Hexachlorocyclohexane degradation
1.25	map00626	Naphthalene and anthracene degradation
1.25	map00632	Benzoate degradation via CoA ligation
1.25	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_XRE domain which could be assigned to a KEGG orthologous group, and not all proteins containing HTH_XRE 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_XRE domains in PDB

PDB code	Title
1adr	Determination of the nuclear magnetic resonance structure of the dna-binding domain of the p22 c2 repressor (1-76) in solution and comparison with the dna-binding domain of the 434 repressor
1b0n	Sinr protein/sini protein complex
1lli	The crystal structure of a mutant protein with altered but improved hydrophobic core packing
1lmb	Refined 1.8 angstrom crystal structure of the lambda repressor-operator complex
1lrp	Comparison of the structures of cro and lambda repressor proteins from bacteriophage lambda
1per	The complex between phage 434 repression dna-binding domain and operator site or3: structural differences between consensus and non-consensus half-sites
1pra	Determination of the nuclear magnetic resonance solution structure of the dna-binding domain (residues 1 to 69) of the 434 repressor and comparison with the x-ray crystal structure
1r63	Structural role of a buried salt bridge in the 434 repressor dna-binding domain, nmr, 20 structures
1r69	Structure of the amino-terminal domain of phage 434 repressor at 2.0 angstroms resolution
1rio	Structure of bacteriophage lambda ci-ntd in complex with sigma-region4 of thermus aquaticus bound to dna
1rpe	The phage 434 or2/r1-69 complex at 2.5 angstroms resolution
1sq8	A variant 434 repressor dna binding domain devoid of hydroxyl groups, nmr, 20 structures
1utx	Regulation of cytolysin expression by enterococcus faecalis: role of cylr2
1x57	Solution structures of the hth domain of human edf-1 protein
1y7y	High-resolution crystal structure of the restriction- modification controller protein c.ahdi from aeromonas hydrophila
1y9q	Crystal structure of hth_3 family transcriptional regulator from vibrio cholerae
1zug	Structure of phage 434 cro protein, nmr, 20 structures
1zz6	Crystal structure of apo-hppe
1zz7	Crystal structure of feii hppe in complex with substrate form 1
1zz8	Crystal structure of feii hppe in complex with substrate form 2
1zz9	Crystal structure of feii hppe
1zzb	Crystal structure of coii hppe in complex with substrate
1zzc	Crystal structure of coii hppe in complex with tris buffer
2a6c	Crystal structure of (np_841403.1) from nitrosomonas europaea at 1.90 a resolution
2aw6	Structure of a bacterial peptide pheromone/receptor complex and its mechanism of gene regulation
2awi	Structure of prgx y153c mutant
2axu	Structure of prgx
2axv	Structure of prgx y153c mutant
2axz	Crystal structure of prgx/ccf10 complex
2b5a	C.bcli, control element of the bcli restriction- modification system
2bnm	Structure of a zn enzyme
2bnn	Structure of a zn enzyme
2bno	Structure of a zn enzyme
2cro	Structure of phage 434 cro protein at 2.35 angstroms resolution
2eby	Crystal structure of a hypothetical protein from e. coli
2ef8	Crystal structure of c.ecot38is
2ewt	Crystal structure of the dna-binding domain of bldd
2grl	Crystal structure of dct/icf10 complex
2grm	Crystal structure of prgx/icf10 complex
2gzu	High-resolution structure determination of the cylr2 homodimer using intermonomer distances from paramagnetic relaxation enhancement and nmr dipolar couplings
2icp	Crystal structure of the bacterial antitoxin higa from escherichia coli at ph 4.0. northeast structural genomics consortium target er390.
2ict	Crystal structure of the bacterial antitoxin higa from escherichia coli at ph 8.5. northeast structural genomics target er390.
2jvl
2k9q
2kpj
2o38	Putative xre family transcriptional regulator
2ofy	Crystal structure of putative xre-family transcriptional regulator from rhodococcus sp.
2or1	Recognition of a dna operator by the repressor of phage 434. a view at high resolution
2p5t	Molecular and structural characterization of the pezat chromosomal toxin-antitoxin system of the human pathogen streptococcus pneumoniae
2ppx	Crystal structure of a hth xre-family like protein from agrobacterium tumefaciens
2qfc	Crystal structure of bacillus thuringiensis plcr complexed with papr
2r1j	Crystal structure of the p22 c2 repressor protein in complex with the synthetic operator 9t
2r63	Structural role of a buried salt bridge in the 434 repressor dna-binding domain, nmr, 20 structures
2wiu
3b7h	Crystal structure of the prophage lp1 protein 11
3bdn	Crystal structure of the lambda repressor
3bs3	Crystal structure of a putative dna-binding protein from bacteroides fragilis
3cec	Crystal structure of putative antidote protein of plasmid maintenance system (zp_00107635.1) from nostoc punctiforme pcc 73102 at 1.60 a resolution
3clc	Crystal structure of the restriction-modification controller protein c.esp1396i tetramer in complex with its natural 35 base-pair operator
3cro	The phage 434 cro/or1 complex at 2.5 angstroms resolution
3dnv
3eus
3f51
3f52
3f6w
3fya
3g5g
3g7d
3gbf
3hzi
3ivp

Links (links to other resources describing this domain)

• PFAM: HTH_3
• INTERPRO: IPR001387