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| | <StructureSection load='5t4j' size='340' side='right'caption='[[5t4j]], [[Resolution|resolution]] 2.23Å' scene=''> | | <StructureSection load='5t4j' size='340' side='right'caption='[[5t4j]], [[Resolution|resolution]] 2.23Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5t4j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T4J FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5t4j]] is a 1 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=5T4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T4J FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABU:GAMMA-AMINO-BUTANOIC+ACID'>ABU</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.231Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gabR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ABU:GAMMA-AMINO-BUTANOIC+ACID'>ABU</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> |
| - | <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=5t4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t4j OCA], [http://pdbe.org/5t4j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t4j RCSB], [http://www.ebi.ac.uk/pdbsum/5t4j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t4j ProSAT]</span></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=5t4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t4j OCA], [https://pdbe.org/5t4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t4j RCSB], [https://www.ebi.ac.uk/pdbsum/5t4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t4j 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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| | </div> | | </div> |
| | <div class="pdbe-citations 5t4j" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5t4j" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Vibrio subtilis ehrenberg 1835]] | + | [[Category: Bacillus subtilis]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Belitsky, B R]] | + | [[Category: Belitsky BR]] |
| - | [[Category: Farley, M]] | + | [[Category: Farley M]] |
| - | [[Category: Juncosa, J I]] | + | [[Category: Juncosa JI]] |
| - | [[Category: Le, H V]] | + | [[Category: Le HV]] |
| - | [[Category: Lehrer, H J.S]] | + | [[Category: Lehrer HJS]] |
| - | [[Category: Liu, D]] | + | [[Category: Liu D]] |
| - | [[Category: Petsko, G A]] | + | [[Category: Petsko GA]] |
| - | [[Category: Ringe, D]] | + | [[Category: Ringe D]] |
| - | [[Category: Sanishvili, R]] | + | [[Category: Sanishvili R]] |
| - | [[Category: Silverman, R B]] | + | [[Category: Silverman RB]] |
| - | [[Category: Wu, R]] | + | [[Category: Wu R]] |
| - | [[Category: External aldimine]]
| + | |
| - | [[Category: Gaba]]
| + | |
| - | [[Category: Gabr]]
| + | |
| - | [[Category: Mocr]]
| + | |
| - | [[Category: Plp]]
| + | |
| - | [[Category: Transcription regulator]]
| + | |
| 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
The Bacillus subtilis protein regulator of the gabTD operon and its own gene (GabR) is a transcriptional activator that regulates transcription of gamma-aminobutyric acid aminotransferase (GABA-AT; GabT) upon interactions with pyridoxal-5'-phosphate (PLP) and GABA, and thereby promotes the biosynthesis of glutamate from GABA. We show here that the external aldimine formed between PLP and GABA is apparently responsible for triggering the GabR-mediated transcription activation. Details of the "active site" in the structure of the GabR effector-binding/oligomerization (Eb/O) domain suggest that binding a monocarboxylic gamma-amino acid such as GABA should be preferred over dicarboxylic acid ligands. A reactive GABA analog, (S)-4-amino-5-fluoropentanoic acid (AFPA), was used as a molecular probe to examine the reactivity of PLP in both GabR and a homologous aspartate aminotransferase (Asp-AT) from Escherichia coli as a control. A comparison between the structures of the Eb/O-PLP-AFPA complex and Asp-AT-PLP-AFPA complex revealed that GabR is incapable of facilitating further steps of the transamination reaction after the formation of the external aldimine. Results of in vitro and in vivo assays using full-length GabR support the conclusion that AFPA is an agonistic ligand capable of triggering GabR-mediated transcription activation via formation of an external aldimine with PLP.
PLP and GABA trigger GabR-mediated transcription regulation in Bacillus subtilis via external aldimine formation.,Wu R, Sanishvili R, Belitsky BR, Juncosa JI, Le HV, Lehrer HJ, Farley M, Silverman RB, Petsko GA, Ringe D, Liu D Proc Natl Acad Sci U S A. 2017 Mar 27. pii: 201703019. doi:, 10.1073/pnas.1703019114. PMID:28348215[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
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
- ↑ Wu R, Sanishvili R, Belitsky BR, Juncosa JI, Le HV, Lehrer HJ, Farley M, Silverman RB, Petsko GA, Ringe D, Liu D. PLP and GABA trigger GabR-mediated transcription regulation in Bacillus subtilis via external aldimine formation. Proc Natl Acad Sci U S A. 2017 Mar 27. pii: 201703019. doi:, 10.1073/pnas.1703019114. PMID:28348215 doi:http://dx.doi.org/10.1073/pnas.1703019114
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