HTH_XREHelix-turn-helix XRE-family like proteins
|SMART accession number:||SM00530|
|Interpro abstract (IPR001387):|
The cro/C1-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 residues present in transcriptional regulators. The domain is named after the transcriptional repressors cro and C1 of temperate bacteriophages 434 and lambda, respectively. Besides in bacteriophages, cro/C1-type regulators are present in prokaryotes and in eukaryotes. The helix-turn-helix DNA-binding motif is generally located in the N-terminal part of these transcriptional regulators. The C-terminal part may contain an oligomerization domain, e.g. C1 repressors and CopR act as dimers, while SinR is a tetramer. The cro/C1-type HTH domain also occurs in combination with the TPR repeat and the C-terminal part of C-5 cytosine-specific DNA methylases contains regions related to the enzymatic function.
Several structures of cro/C1-type transcriptional repressors have been resolved and their DNA-binding domain encompasses five alpha helices, of which the extremities are less conserved [(PUBMED:3187531)]. The helix-turn-helix motif comprises the second and third helices, the third being called the recognition helix. The HTH is involved in DNA-binding into the major groove, where the recognition helix makes most DNA-contacts. The bacteriophage repressors regulate lysogeny/lytic growth by binding with differential affinity to the operators. These operators show 2-fold symmetry and the repressors bind as dimers. Binding of the repressor to the operator positions the DNA backbone into a slightly bent twist [(PUBMED:3187531), (PUBMED:11972345)].
|GO function:||sequence-specific DNA binding (GO:0043565)|
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- Evolution (species in which this domain is found)
Taxonomic distribution of proteins containing HTH_XRE domain.
This tree includes only several representative species. The complete taxonomic breakdown of all proteins with HTH_XRE domain is also avaliable.
Click on the protein counts, or double click on taxonomic names to display all proteins containing HTH_XRE domain in the selected taxonomic class.
- 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
- Display abstract
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
- Display abstract
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)
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% 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 Main view 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 A PUTATIVE TRANSCRIPTIONAL REGULATOR (NE_1354) 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 The structure of Hydroxypropylphosphonic acid epoxidase from S. wedmorenis. 2bnn The structure of Hydroxypropylphosphonic acid epoxidase from S. wedmorenis in complex with fosfomycin 2bno The structure of Hydroxypropylphosphonic acid epoxidase from S. wedmorenis 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 NMR structure of the C-terminal domain of MBF1 of Trichoderma reesei 2k9q Solution NMR structure of HTH_XRE family transcriptional regulator BT_p548217 from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium Target BtR244. 2kpj Solution Structure Of Protein SOS-response transcriptional repressor, LexA From Eubacterium rectale. Northeast Structural Genomics Consortium Target ErR9A 2kz8 Solution NMR structure of MqsA, a protein from E. coli, containing a Zinc finger, N-terminal and a Helix Turn-Helix C-terminal domain 2l49 The solution structure of the P2 C,the immunity repressor of the P2 bacteriophage 2lyj NOE-based 3D structure of the CylR2 homodimer at 298K 2lyk NOE-based 3D structure of the CylR2 homodimer at 270K (-3 Celsius degrees) 2lyl NOE-based 3D structure of the predissociated homodimer of CylR2 in equilibrium with monomer at 266K (-7 Celsius degrees) 2lyp NOE-based 3D structure of the monomer of CylR2 in equilibrium with predissociated homodimer at 266K (-7 Celsius degrees) 2lyq NOE-based 3D structure of the monomeric intermediate of CylR2 at 262K (-11 Celsius degrees) 2lyr NOE-based 3D structure of the monomeric partially-folded intermediate of CylR2 at 259K (-14 Celsius degrees) 2lys NOE-based 3D structure of the monomeric partially-folded intermediate of CylR2 at 257K (-16 Celsius degrees) 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 Mercury-modified bacterial persistence regulator hipBA 2xcj Crystal structure of P2 C, the immunity repressor of temperate E. coli phage P2 2xi8 High resolution structure of native CylR2 2xiu High resolution structure of MTSL-tagged CylR2. 2xj3 High resolution structure of the T55C mutant of CylR2. 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 a putative antidote protein of plasmid maintenance system (npun_f2943) 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 MDT Protein 3eus The crystal structure of the DNA binding protein from Silicibacter pomeroyi 3f51 Crystal Structure of the clp gene regulator ClgR from Corynebacterium glutamicum 3f52 Crystal structure of the clp gene regulator ClgR from C. glutamicum 3f6w XRE-family like protein from Pseudomonas syringae pv. tomato str. DC3000 3fmy Structure of the C-terminal domain of the E. coli protein MQSA (YgiT/b3021) 3fya Crystal Structure of an R35A mutant of the Restriction-Modification Controller Protein C.Esp1396I 3fym The 1A structure of YmfM, a putative DNA-binding membrane protein from Staphylococcus aureus 3g5g Crystal Structure of the Wild-Type Restriction-Modification Controller Protein C.Esp1396I 3g7d Native PhpD with Cadmium Atoms 3gbf Phpd with cadmium complexed with hydroethylphosphonate (HEP) 3gn5 Structure of the E. coli protein MqsA (YgiT/b3021) 3hzi Structure of mdt protein 3ivp The structure of a possible transposon-related DNA-binding protein from Clostridium difficile 630. 3jxb Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C 3jxc Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9T in the presence of Tl+ 3jxd Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C in the presence of Rb+ 3kxa Crystal Structure of NGO0477 from Neisseria gonorrhoeae 3kz3 A structure of a lambda repressor fragment mutant 3lfp Crystal Structure of the Restriction-Modification Controller Protein C.Csp231I 3lis Crystal Structure of the Restriction-Modification Controller Protein C.Csp231I (Monoclinic form) 3mlf Putative transcriptional regulator from Staphylococcus aureus. 3o9x Structure of the E. coli antitoxin MqsA (YgiT/b3021) in complex with its gene promoter 3omt Putative antitoxin component, CHU_2935 protein, from Xre family from Prevotella buccae. 3op9 Crystal structure of transcriptional regulator from Listeria innocua 3pxp Crystal structure of a PAS and DNA binding domain containing protein (Caur_2278) from CHLOROFLEXUS AURANTIACUS J-10-FL at 2.30 A resolution 3qq6 The N-terminal DNA binding domain of SinR from Bacillus subtilis 3rzz Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant 3s8q Crystal structure of the R-M controller protein C.Esp1396I OL operator complex 3scf Fe(II)-HppE with S-HPP and NO 3scg Fe(II)-HppE with R-HPP 3sch Co(II)-HppE with R-HPP 3trb Structure of an addiction module antidote protein of a HigA (higA) family from Coxiella burnetii 3u3w Crystal Structure of Bacillus thuringiensis PlcR in complex with the peptide PapR7 and DNA 3ufd C.Esp1396I bound to its highest affinity operator site OM 3vk0 Crystal Structure of hypothetical transcription factor NHTF from Neisseria 3zhi N-terminal domain of the CI repressor from bacteriophage TP901-1 3zhm N-terminal domain of the CI repressor from bacteriophage TP901-1 in complex with the OL2 operator half-site 3zkc Crystal structure of the master regulator for biofilm formation SinR in complex with DNA. 4f8d Crystal Structure of an R46A mutant of the Restriction-Modification Controller Protein C.Esp1396I (Monoclinic Form) 4fbi Crystal Structure of an R46A mutant of the Restriction-Modification Controller Protein C.Esp1396I (Trigonal Form) 4fn3 Crystal Structure of an S52A mutant of the Restriction-Modification Controller Protein C.Esp1396I 4fsc Crystal Structure of Bacillus thuringiensis PlcR in its apo form 4ghj 1.75 Angstrom Crystal Structure of Transcriptional Regulator ftom Vibrio vulnificus. 4gqm Crystal structure of a helix-turn-helix containing hypothetical protein (CT009) from Chlamydia trachomatis in a sub-domain swap conformation 4i6r High Resolution Crystal Structure of the Wild-Type Restriction-Modification Controller Protein C.Esp1396I (Triclinic form) 4i6t Crystal Structure of a T36A mutant of the Restriction-Modification Controller Protein C.Esp1396I 4i6u Crystal Structure of a Y37F mutant of the Restriction-Modification Controller Protein C.Esp1396I 4i8t C.Esp1396I bound to a 19 base pair DNA duplex 4ia8 Crystal Structure of a Y37A mutant of the Restriction-Modification Controller Protein C.Esp1396I 4ivz A Y37F mutant of C.Esp1396I bound to its highest affinity operator site OM 4iwr C.Esp1396I bound to a 25 base pair operator site 4j1w Crystal Structure of Fe(II)-HppE with alternative substrate (R)-1-HPP 4j1x Crystal Structure of Fe(II)-HppE with alternative substrate (S)-1-HPP 4jcx Crystal structure of the Restriction-Modification Controller Protein C.Csp231I OL operator complex 4jcy Crystal structure of the Restriction-Modification Controller Protein C.Csp231I OR operator complex 4jqd Crystal structure of the Restriction-Modification Controller Protein C.Csp231I OL operator complex 4mct P. vulgaris HIGBA structure, crystal form 1 4mcx P. vulgaris HIGBA structure, crystal form 2 4o8b Crystal structure of transcriptional regulator BswR
- Links (links to other resources describing this domain)
PFAM HTH_3 INTERPRO IPR001387