SMART: HTH_XRE domain annotation

HTH_XRE Helix-turn-helix XRE-family like proteins

SMART accession number:	SM00530
Description:	-
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) ].
Family alignment:	View or

There are 375913 HTH_XRE domains in 370972 proteins in SMART's nrdb database.

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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)

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)
2mez		2MEZ
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		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
3tyr		Crystal structure of transcriptional regulator VanUg, Form I
3tys		Crystal structure of transcriptional regulator VanUg, Form II
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
4ich		Crystal structure of a putative TetR family transcriptional regulator from Saccharomonospora viridis DSM 43017
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
4ob4		4OB4
4pu3		4PU3
4pu4		4PU4
4pu7		4PU7
4pu8		4PU8
4ryk		4RYK
4x4b		4X4B
4x4c		4X4C
4x4d		4X4D
4x4e		4X4E
4x4f		4X4F
4x4g		4X4G
4x4h		4X4H
4x4i		4X4I
4yar		4YAR
4yba		4YBA
4yg1		4YG1
4yg4		4YG4
4yg7		4YG7
4yv6		4YV6
4yv9		4YV9
4z58		4Z58
4z59		4Z59
4z5c		4Z5C
4z5d		4Z5D
4z5h		4Z5H
5a7l		5A7L
5fd4		5FD4
5jub		5JUB
5juf		5JUF
5k98		5K98

Links (links to other resources describing this domain)
PFAM HTH_3
INTERPRO IPR001387

PFAM	HTH_3
INTERPRO	IPR001387

HTH_XRE

Taxonomic distribution of proteins containing HTH_XRE domain.

3D Structures of HTH_XRE domains in PDB