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| | ==Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of GabT== | | ==Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of GabT== |
| - | <StructureSection load='4n0b' size='340' side='right' caption='[[4n0b]], [[Resolution|resolution]] 2.71Å' scene=''> | + | <StructureSection load='4n0b' size='340' side='right'caption='[[4n0b]], [[Resolution|resolution]] 2.71Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4n0b]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N0B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4N0B FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4n0b]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N0B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N0B FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4n0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n0b OCA], [https://pdbe.org/4n0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n0b RCSB], [https://www.ebi.ac.uk/pdbsum/4n0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n0b ProSAT]</span></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4mgr|4mgr]]</td></tr>
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| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gabR, ycnF, BSU03890 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4n0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n0b OCA], [http://pdbe.org/4n0b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4n0b RCSB], [http://www.ebi.ac.uk/pdbsum/4n0b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4n0b ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/GABR_BACSU GABR_BACSU]] Activates the transcription of the gabTD operon. Is also a repressor of its own expression, both in the presence and absence of GABA. Binds specifically to the DNA region overlapping the -35 region of the gabT promoter and the -10 and +1 regions of the gabR promoter. Principally regulates the utilization of gamma-aminobutyrate.<ref>PMID:12123465</ref> <ref>PMID:15223311</ref> | + | [https://www.uniprot.org/uniprot/GABR_BACSU GABR_BACSU] Activates the transcription of the gabTD operon. Is also a repressor of its own expression, both in the presence and absence of GABA. Binds specifically to the DNA region overlapping the -35 region of the gabT promoter and the -10 and +1 regions of the gabR promoter. Principally regulates the utilization of gamma-aminobutyrate.<ref>PMID:12123465</ref> <ref>PMID:15223311</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus globigii migula 1900]] | + | [[Category: Bacillus subtilis]] |
| - | [[Category: Bach, A]] | + | [[Category: Large Structures]] |
| - | [[Category: Belitsky, B R]] | + | [[Category: Bach A]] |
| - | [[Category: Edayathumangalam, R]] | + | [[Category: Belitsky BR]] |
| - | [[Category: Garcia, R]] | + | [[Category: Edayathumangalam R]] |
| - | [[Category: Hoang, Q Q]] | + | [[Category: Garcia R]] |
| - | [[Category: Kreinbring, C A]] | + | [[Category: Hoang QQ]] |
| - | [[Category: Liao, J]] | + | [[Category: Kreinbring CA]] |
| - | [[Category: Liu, D]] | + | [[Category: Liao J]] |
| - | [[Category: Petsko, G A]] | + | [[Category: Liu D]] |
| - | [[Category: Ringe, D]] | + | [[Category: Petsko GA]] |
| - | [[Category: Stone, T]] | + | [[Category: Ringe D]] |
| - | [[Category: Terwilliger, T]] | + | [[Category: Stone T]] |
| - | [[Category: Wang, W]] | + | [[Category: Terwilliger T]] |
| - | [[Category: Wang, Y]] | + | [[Category: Wang W]] |
| - | [[Category: Wu, R]] | + | [[Category: Wang Y]] |
| - | [[Category: Activator]]
| + | [[Category: Wu R]] |
| - | [[Category: Autorepressor]]
| + | |
| - | [[Category: Transcription activator]]
| + | |
| - | [[Category: Transcription factor]]
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| - | [[Category: Type-i aminotransferase-like fold]]
| + | |
| - | [[Category: Winged helix domain]]
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| Structural highlights
Function
GABR_BACSU Activates the transcription of the gabTD operon. Is also a repressor of its own expression, both in the presence and absence of GABA. Binds specifically to the DNA region overlapping the -35 region of the gabT promoter and the -10 and +1 regions of the gabR promoter. Principally regulates the utilization of gamma-aminobutyrate.[1] [2]
Publication Abstract from PubMed
Bacillus subtilis GabR is a transcription factor that regulates gamma-aminobutyric acid (GABA) metabolism. GabR is a member of the understudied MocR/GabR subfamily of the GntR family of transcription regulators. A typical MocR/GabR-type regulator is a chimeric protein containing a short N-terminal helix-turn-helix DNA-binding domain and a long C-terminal pyridoxal 5'-phosphate (PLP)-binding putative aminotransferase domain. In the presence of PLP and GABA, GabR activates the gabTD operon, which allows the bacterium to use GABA as nitrogen and carbon sources. GabR binds to its own promoter and represses gabR transcription in the absence of GABA. Here, we report two crystal structures of full-length GabR from B. subtilis: a 2.7-A structure of GabR with PLP bound and the 2.55-A apo structure of GabR without PLP. The quaternary structure of GabR is a head-to-tail domain-swap homodimer. Each monomer comprises two domains: an N-terminal winged-helix DNA-binding domain and a C-terminal PLP-binding type I aminotransferase-like domain. The winged-helix domain contains putative DNA-binding residues conserved in other GntR-type regulators. Together with sedimentation velocity and fluorescence polarization assays, the crystal structure of GabR provides insights into DNA binding by GabR at the gabR and gabT promoters. The absence of GabR-mediated aminotransferase activity in the presence of GABA and PLP, and the presence of an active site configuration that is incompatible with stabilization of the GABA external aldimine suggest that a GabR aminotransferase-like activity involving GABA and PLP is not essential to its primary function as a transcription regulator.
Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of gabT.,Edayathumangalam R, Wu R, Garcia R, Wang Y, Wang W, Kreinbring CA, Bach A, Liao J, Stone TA, Terwilliger TC, Hoang QQ, Belitsky BR, Petsko GA, Ringe D, Liu D Proc Natl Acad Sci U S A. 2013 Oct 14. PMID:24127574[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Belitsky BR, Sonenshein AL. GabR, a member of a novel protein family, regulates the utilization of gamma-aminobutyrate in Bacillus subtilis. Mol Microbiol. 2002 Jul;45(2):569-83. PMID:12123465
- ↑ Belitsky BR. Bacillus subtilis GabR, a protein with DNA-binding and aminotransferase domains, is a PLP-dependent transcriptional regulator. J Mol Biol. 2004 Jul 16;340(4):655-64. PMID:15223311 doi:http://dx.doi.org/10.1016/j.jmb.2004.05.020
- ↑ Edayathumangalam R, Wu R, Garcia R, Wang Y, Wang W, Kreinbring CA, Bach A, Liao J, Stone TA, Terwilliger TC, Hoang QQ, Belitsky BR, Petsko GA, Ringe D, Liu D. Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of gabT. Proc Natl Acad Sci U S A. 2013 Oct 14. PMID:24127574 doi:http://dx.doi.org/10.1073/pnas.1315887110
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