3qq6: Difference between revisions

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<StructureSection load='3qq6' size='340' side='right'caption='[[3qq6]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='3qq6' size='340' side='right'caption='[[3qq6]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3qq6]] is a 2 chain structure with sequence from [https://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=3QQ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QQ6 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3qq6]] is a 2 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=3QQ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QQ6 FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1b0n|1b0n]]</div></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]] 1.9&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU24610, flaD, sin, sinR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=3qq6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qq6 OCA], [https://pdbe.org/3qq6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qq6 RCSB], [https://www.ebi.ac.uk/pdbsum/3qq6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qq6 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=3qq6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qq6 OCA], [https://pdbe.org/3qq6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qq6 RCSB], [https://www.ebi.ac.uk/pdbsum/3qq6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qq6 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/SINR_BACSU SINR_BACSU]] Negative as well as positive regulator of alternate developmental processes that are induced at the end of vegetative growth in response to nutrient depletion. Binds to the alkaline protease (aprE) gene at two sites. Also acts as a repressor of the key sporulation gene spo0A. Negatively regulates transcription of the eps operon, which is responsible for the biosynthesis of an exopolysaccharide involved in biofilm formation; therefore it could govern the transition between a state in which bacteria swim or swarm and a state in which bacteria assemble into multicellular communities. Acts with Hpr as a corepressor of epr expression. Also negatively regulates transcription of the lutABC operon, which is required for lactate utilization. Repressor activity is regulated by SinI.<ref>PMID:1898931</ref> <ref>PMID:7642487</ref> <ref>PMID:15661000</ref> <ref>PMID:16923912</ref> 
[https://www.uniprot.org/uniprot/SINR_BACSU SINR_BACSU] Negative as well as positive regulator of alternate developmental processes that are induced at the end of vegetative growth in response to nutrient depletion. Binds to the alkaline protease (aprE) gene at two sites. Also acts as a repressor of the key sporulation gene spo0A. Negatively regulates transcription of the eps operon, which is responsible for the biosynthesis of an exopolysaccharide involved in biofilm formation; therefore it could govern the transition between a state in which bacteria swim or swarm and a state in which bacteria assemble into multicellular communities. Acts with Hpr as a corepressor of epr expression. Also negatively regulates transcription of the lutABC operon, which is required for lactate utilization. Repressor activity is regulated by SinI.<ref>PMID:1898931</ref> <ref>PMID:7642487</ref> <ref>PMID:15661000</ref> <ref>PMID:16923912</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
sinR encodes a tetrameric repressor of genes required for biofilm formation in Bacillus subtilis. sinI, which is transcribed under Spo0A control, encodes a dimeric protein that binds to SinR to form a SinR-SinI heterodimer in which the DNA-binding functions of SinR are abrogated and repression of biofilm genes is relieved. The heterodimer-forming surface comprises residues conserved between SinR and SinI. Each forms a pair of alpha-helices that hook together to form an intermolecular four-helix bundle. Here, we are interested in the assembly of the SinR tetramer and its binding to DNA. Size-exclusion chromatography with multi-angle laser light scattering and crystallographic analysis reveal that a DNA-binding fragment of SinR (residues 1-69) is a monomer, while a SinI-binding fragment (residues 74-111) is a tetramer arranged as a dimer of dimers. The SinR(74-111) chain forms two alpha-helices with the organisation of the dimer similar to that observed in the SinR-SinI complex. The tetramer is formed through interactions of residues at the C-termini of the four chains. A model of the intact SinR tetramer in which the DNA binding domains surround the tetramerisation core was built. Fluorescence anisotropy and surface plasmon resonance experiments showed that SinR binds to an oligonucleotide duplex, 5'-TTTGTTCTCTAAAGAGAACTTA-3', containing a pair of SinR consensus sequences in inverted orientation with a K(d) of 300 nM. The implications of these data for promoter binding and the curious quaternary structural transitions of SinR upon binding to (i) SinI and (ii) the SinR-like protein SlrR, which "repurposes" SinR as a repressor of autolysin and motility genes, are discussed.
 
Structure and Organisation of SinR, the Master Regulator of Biofilm Formation in Bacillus subtilis.,Colledge VL, Fogg MJ, Levdikov VM, Leech A, Dodson EJ, Wilkinson AJ J Mol Biol. 2011 Aug 19;411(3):597-613. Epub 2011 Jun 25. PMID:21708175<ref>PMID:21708175</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3qq6" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Vibrio subtilis ehrenberg 1835]]
[[Category: Bacillus subtilis]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Colledge, V]]
[[Category: Colledge V]]
[[Category: Dodson, E J]]
[[Category: Dodson EJ]]
[[Category: Fogg, M J]]
[[Category: Fogg MJ]]
[[Category: Levdikov, V M]]
[[Category: Levdikov VM]]
[[Category: Wilkinson, A J]]
[[Category: Wilkinson AJ]]
[[Category: Biofilm]]
[[Category: Helix-turn-helix motif]]
[[Category: Repressor]]
[[Category: Sini]]
[[Category: Transcription]]
[[Category: Transcriptional regulator]]

Latest revision as of 14:54, 14 March 2024

The N-terminal DNA binding domain of SinR from Bacillus subtilisThe N-terminal DNA binding domain of SinR from Bacillus subtilis

Structural highlights

3qq6 is a 2 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SINR_BACSU Negative as well as positive regulator of alternate developmental processes that are induced at the end of vegetative growth in response to nutrient depletion. Binds to the alkaline protease (aprE) gene at two sites. Also acts as a repressor of the key sporulation gene spo0A. Negatively regulates transcription of the eps operon, which is responsible for the biosynthesis of an exopolysaccharide involved in biofilm formation; therefore it could govern the transition between a state in which bacteria swim or swarm and a state in which bacteria assemble into multicellular communities. Acts with Hpr as a corepressor of epr expression. Also negatively regulates transcription of the lutABC operon, which is required for lactate utilization. Repressor activity is regulated by SinI.[1] [2] [3] [4]

References

  1. ↑ Gaur NK, Oppenheim J, Smith I. The Bacillus subtilis sin gene, a regulator of alternate developmental processes, codes for a DNA-binding protein. J Bacteriol. 1991 Jan;173(2):678-86. PMID:1898931
  2. ↑ Mandic-Mulec I, Doukhan L, Smith I. The Bacillus subtilis SinR protein is a repressor of the key sporulation gene spo0A. J Bacteriol. 1995 Aug;177(16):4619-27. PMID:7642487
  3. ↑ Kearns DB, Chu F, Branda SS, Kolter R, Losick R. A master regulator for biofilm formation by Bacillus subtilis. Mol Microbiol. 2005 Feb;55(3):739-49. PMID:15661000 doi:10.1111/j.1365-2958.2004.04440.x
  4. ↑ Kodgire P, Dixit M, Rao KK. ScoC and SinR negatively regulate epr by corepression in Bacillus subtilis. J Bacteriol. 2006 Sep;188(17):6425-8. PMID:16923912 doi:10.1128/JB.00427-06

3qq6, resolution 1.90Å

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