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74  structures 4244  species 2  interactions 38873  sequences 273  architectures

Family: GerE (PF00196)

Summary: Bacterial regulatory proteins, luxR family

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This is the Wikipedia entry entitled "LuxR-type DNA-binding HTH domain". More...

LuxR-type DNA-binding HTH domain Edit Wikipedia article

Bacterial regulatory proteins, luxR family
PDB 1p4w EBI.jpg
solution structure of the dna-binding domain of the erwinia amylovora rcsb protein
Identifiers
Symbol GerE
Pfam PF00196
Pfam clan CL0123
InterPro IPR000792
PROSITE PDOC00542
SCOP 1rnl
SUPERFAMILY 1rnl

In molecular biology, the LuxR-type DNA-binding HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids. It is present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region of the protein; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes.

The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers.[1][2][3]

LuxR-type HTH proteins can be activated by one of four different mechanisms:

1. Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase.[4][5] Some proteins that belong to this category are:

2. Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria:[6]

  • E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes)
  • Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene)

3. Autonomous effector domain regulators, without a regulatory domain, represented by gerE.[1]

4. Multiple ligand-binding regulators, exemplified by malT.[7]

References[edit]

  1. ^ a b Ducros VM, Lewis RJ, Verma CS, Dodson EJ, Leonard G, Turkenburg JP, Murshudov GN, Wilkinson AJ, Brannigan JA (March 2001). "Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis". J. Mol. Biol. 306 (4): 759–71. doi:10.1006/jmbi.2001.4443. PMID 11243786. 
  2. ^ Pristovsek P, Sengupta K, Lohr F, Schafer B, von Trebra MW, Ruterjans H, Bernhard F (May 2003). "Structural analysis of the DNA-binding domain of the Erwinia amylovora RcsB protein and its interaction with the RcsAB box". J. Biol. Chem. 278 (20): 17752–9. doi:10.1074/jbc.M301328200. PMID 12740396. 
  3. ^ Zhang RG, Pappas T, Brace JL, Miller PC, Oulmassov T, Molyneaux JM, Anderson JC, Bashkin JK, Winans SC, Joachimiak A (June 2002). "Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA". Nature 417 (6892): 971–4. doi:10.1038/nature00833. PMID 12087407. 
  4. ^ Maris AE, Sawaya MR, Kaczor-Grzeskowiak M, Jarvis MR, Bearson SM, Kopka ML, Schroder I, Gunsalus RP, Dickerson RE (October 2002). "Dimerization allows DNA target site recognition by the NarL response regulator". Nat. Struct. Biol. 9 (10): 771–8. doi:10.1038/nsb845. PMID 12352954. 
  5. ^ Birck C, Malfois M, Svergun D, Samama J (August 2002). "Insights into signal transduction revealed by the low resolution structure of the FixJ response regulator". J. Mol. Biol. 321 (3): 447–57. doi:10.1016/S0022-2836(02)00651-4. PMID 12162958. 
  6. ^ Pappas KM, Weingart CL, Winans SC (August 2004). "Chemical communication in proteobacteria: biochemical and structural studies of signal synthases and receptors required for intercellular signalling". Mol. Microbiol. 53 (3): 755–69. doi:10.1111/j.1365-2958.2004.04212.x. PMID 15255890. 
  7. ^ Schlegel A, Bohm A, Lee SJ, Peist R, Decker K, Boos W (May 2002). "Network regulation of the Escherichia coli maltose system". J. Mol. Microbiol. Biotechnol. 4 (3): 301–7. PMID 11931562. 

This article incorporates text from the public domain Pfam and InterPro IPR000792

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Bacterial regulatory proteins, luxR family Provide feedback

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This tab holds annotation information from the InterPro database.

InterPro entry IPR000792

This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes.

The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [PUBMED:11243786, PUBMED:12740396, PUBMED:12087407].

LuxR-type HTH proteins can be activated by one of four different mechanisms:

1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [PUBMED:12352954, PUBMED:12162958]. Some proteins that belong to this category are:

  • Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis)
  • Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT)
  • E. coli narL and narP (activate nitrate reductase operon)
  • Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis)
  • Bordetella pertussis bvgA (virulence factor)
  • Bacillus subtilis coma (involved in expression of late-expressing competence genes)
  • 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria [PUBMED:15255890]:

  • V. fischeri luxR (activates bioluminescence operon)
  • Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer)
  • Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis)
  • E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes)
  • Pseudomonas aeruginosa lasR (activates elastase gene lasB)
  • Erwinia chrysanthemi echR and Erwinia stewartii esaR
  • Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production)
  • Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene)
  • 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE [PUBMED:11243786].

  • B. subtilis gerE (transcription activator and repressor for the regulation of spore formation)
  • 4) Multiple ligand-binding regulators, exemplified by malT [PUBMED:11931562].

  • E. coli malT (activates maltose operon; MalT binds ATP and maltotriose)
  • Gene Ontology

    The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

    Domain organisation

    Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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    Pfam Clan

    This family is a member of clan HTH (CL0123), which has the following description:

    This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif.

    The clan contains the following 202 members:

    AphA_like Arg_repressor B-block_TFIIIC Bac_DnaA_C BetR Bot1p BrkDBD CENP-B_N Cro Crp DDRGK Dimerisation DUF1133 DUF1153 DUF1323 DUF134 DUF1441 DUF1492 DUF1495 DUF1670 DUF1804 DUF1836 DUF1870 DUF2089 DUF2250 DUF2316 DUF3116 DUF3853 DUF387 DUF3908 DUF4095 DUF4364 DUF739 DUF742 DUF977 E2F_TDP ELK Ets Exc F-112 FaeA Fe_dep_repr_C Fe_dep_repress FeoC Ftsk_gamma FUR GcrA GerE GntR HARE-HTH HemN_C Homeobox Homeobox_KN Homez HrcA_DNA-bdg HSF_DNA-bind HTH_1 HTH_10 HTH_11 HTH_12 HTH_13 HTH_15 HTH_16 HTH_17 HTH_18 HTH_19 HTH_20 HTH_21 HTH_22 HTH_23 HTH_24 HTH_25 HTH_26 HTH_27 HTH_28 HTH_29 HTH_3 HTH_30 HTH_31 HTH_32 HTH_33 HTH_34 HTH_35 HTH_36 HTH_37 HTH_38 HTH_39 HTH_40 HTH_41 HTH_42 HTH_43 HTH_45 HTH_5 HTH_6 HTH_7 HTH_8 HTH_9 HTH_AraC HTH_AsnC-type HTH_CodY HTH_Crp_2 HTH_DeoR HTH_IclR HTH_Mga HTH_OrfB_IS605 HTH_psq HTH_Tnp_1 HTH_Tnp_1_2 HTH_Tnp_4 HTH_Tnp_IS1 HTH_Tnp_IS630 HTH_Tnp_ISL3 HTH_Tnp_Mu_1 HTH_Tnp_Mu_2 HTH_Tnp_Tc3_1 HTH_Tnp_Tc3_2 HTH_Tnp_Tc5 HTH_WhiA HxlR IF2_N KorB LacI LexA_DNA_bind LZ_Tnp_IS481 MADF_DNA_bdg MarR MarR_2 Med9 MerR MerR-DNA-bind MerR_1 MerR_2 Mga Mnd1 Mor MotA_activ MRP-L20 Myb_DNA-bind_2 Myb_DNA-bind_3 Myb_DNA-bind_4 Myb_DNA-bind_5 Myb_DNA-bind_6 Myb_DNA-binding Neugrin NUMOD1 OST-HTH P22_Cro PaaX PadR PAX PCI PCI_Csn8 Penicillinase_R Phage_AlpA Phage_antitermQ Phage_CI_repr Phage_CII Phage_rep_org_N Phage_terminase Pou Pox_D5 PuR_N Put_DNA-bind_N Rap1-DNA-bind Rep_3 RepA_C RepA_N RepC RepL Replic_Relax RFX_DNA_binding Ribosomal_S25 Rio2_N RNA_pol_Rpc34 RP-C RPA RPA_C RQC Rrf2 RTP SAC3_GANP SgrR_N Sigma54_CBD Sigma54_DBD Sigma70_ECF Sigma70_r2 Sigma70_r3 Sigma70_r4 Sigma70_r4_2 SpoIIID Sulfolobus_pRN TBPIP Terminase_5 TetR_N TFIIE_alpha Tn916-Xis Trans_reg_C TrfA TrmB Trp_repressor UPF0122 z-alpha

    Alignments

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      Seed
    (30)
    Full
    (38873)
    Representative proteomes NCBI
    (30161)
    Meta
    (2583)
    RP15
    (3079)
    RP35
    (6345)
    RP55
    (8321)
    RP75
    (9895)
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      Seed
    (30)
    Full
    (38873)
    Representative proteomes NCBI
    (30161)
    Meta
    (2583)
    RP15
    (3079)
    RP35
    (6345)
    RP55
    (8321)
    RP75
    (9895)
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    Trees

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    Curation and family details

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    Curation View help on the curation process

    Seed source: Prosite
    Previous IDs: none
    Type: Domain
    Author: Finn RD
    Number in seed: 30
    Number in full: 38873
    Average length of the domain: 57.10 aa
    Average identity of full alignment: 31 %
    Average coverage of the sequence by the domain: 20.74 %

    HMM information View help on HMM parameters

    HMM build commands:
    build method: hmmbuild -o /dev/null HMM SEED
    search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
    Model details:
    Parameter Sequence Domain
    Gathering cut-off 20.6 20.6
    Trusted cut-off 20.6 20.6
    Noise cut-off 20.5 20.5
    Model length: 58
    Family (HMM) version: 14
    Download: download the raw HMM for this family

    Species distribution

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    Interactions

    There are 2 interactions for this family. More...

    GerE Response_reg

    Structures

    For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the GerE domain has been found. There are 74 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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