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55  structures 4089  species 3  interactions 49014  sequences 87  architectures

Family: GntR (PF00392)

Summary: Bacterial regulatory proteins, gntR family

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This is the Wikipedia entry entitled "GntR-like bacterial transcription factors". More...

GntR-like bacterial transcription factors Edit Wikipedia article

Bacterial regulatory proteins, gntR family
PDB 1v4r EBI.jpg
solution structure of streptmycal repressor trar
Identifiers
Symbol GntR
Pfam PF00392
Pfam clan CL0123
InterPro IPR000524
PROSITE PDOC00042
SCOP 1e2x
SUPERFAMILY 1e2x

In molecular biology, the GntR-like bacterial transcription factors are a family of transcription factors.

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.[1] Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined.[2] 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. 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.[3]

References[edit]

  1. ^ Haydon DJ, Guest JR (April 1991). "A new family of bacterial regulatory proteins". FEMS Microbiol. Lett. 63 (2-3): 291–5. PMID 2060763. 
  2. ^ van Aalten DM, DiRusso CC, Knudsen J, Wierenga RK (October 2000). "Crystal structure of FadR, a fatty acid-responsive transcription factor with a novel acyl coenzyme A-binding fold". EMBO J. 19 (19): 5167–77. doi:10.1093/emboj/19.19.5167. PMC 302096. PMID 11013219. 
  3. ^ Rigali S, Derouaux A, Giannotta F, Dusart J (April 2002). "Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies". J. Biol. Chem. 277 (15): 12507–15. doi:10.1074/jbc.M110968200. PMID 11756427. 

This article incorporates text from the public domain Pfam and InterPro IPR000524

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Bacterial regulatory proteins, gntR family Provide feedback

This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR [4]. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships [3]. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor [5].

Literature references

  1. Lee MH, Scherer M, Rigali S, Golden JW; , J Bacteriol 2003;185:4315-4325.: PlmA, a new member of the GntR family, has plasmid maintenance functions in Anabaena sp. strain PCC 7120. PUBMED:12867439 EPMC:12867439

  2. Rigali S, Derouaux A, Giannotta F, Dusart J; , J Biol Chem 2002;277:12507-12515.: Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies. PUBMED:11756427 EPMC:11756427

  3. Rigali S, Schlicht M, Hoskisson P, Nothaft H, Merzbacher M, Joris B, Titgemeyer F; , Nucleic Acids Res 2004;32:3418-3426.: Extending the classification of bacterial transcription factors beyond the helix-turn-helix motif as an alternative approach to discover new cis/trans relationships. PUBMED:15247334 EPMC:15247334

  4. Hillerich B, Westpheling J; , J Bacteriol. 2006;188:7477-7487.: A new GntR family transcriptional regulator in streptomyces coelicolor is required for morphogenesis and antibiotic production and controls transcription of an ABC transporter in response to carbon source. PUBMED:16936034 EPMC:16936034

  5. Rigali S, Nothaft H, Noens EE, Schlicht M, Colson S, Muller M, Joris B, Koerten HK, Hopwood DA, Titgemeyer F, van Wezel GP; , Mol Microbiol. 2006;61:1237-1251.: The sugar phosphotransferase system of Streptomyces coelicolor is regulated by the GntR-family regulator DasR and links N-acetylglucosamine metabolism to the control of development. PUBMED:16925557 EPMC:16925557

  6. Gorelik M, Lunin VV, Skarina T, Savchenko A; , Protein Sci. 2006;15:1506-1511.: Structural characterization of GntR/HutC family signaling domain. PUBMED:16672238 EPMC:16672238


External database links

This tab holds annotation information from the InterPro database.

InterPro entry 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 (INTERPRO). 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.

Gene Ontology

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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
(26)
Full
(49014)
Representative proteomes NCBI
(36460)
Meta
(2838)
RP15
(2975)
RP35
(6426)
RP55
(8851)
RP75
(10949)
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  Seed
(26)
Full
(49014)
Representative proteomes NCBI
(36460)
Meta
(2838)
RP15
(2975)
RP35
(6426)
RP55
(8851)
RP75
(10949)
Alignment:
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Sequence:
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  Seed
(26)
Full
(49014)
Representative proteomes NCBI
(36460)
Meta
(2838)
RP15
(2975)
RP35
(6426)
RP55
(8851)
RP75
(10949)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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HMM logo

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite & Pfam-B_6405 (Release 8.0)
Previous IDs: gntR;
Type: Family
Author: Finn RD, Bateman A, Hoskisson PA
Number in seed: 26
Number in full: 49014
Average length of the domain: 63.00 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 23.05 %

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 21.4 21.4
Trusted cut-off 21.4 21.4
Noise cut-off 21.3 21.3
Model length: 64
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

GntR FadR_C FCD

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 GntR domain has been found. There are 55 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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