3bxe

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of effector binding domain of central glycolytic gene regulator (CggR) from Bacillus subtilis in complex with dihydroxyacetone phosphate

Structural highlights

3bxe 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 1.8Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CGGR_BACSU In the absence of glucose, represses the transcription of the gapA operon, which encodes five key glycolytic enzymes. Binds specifically to the cggR-gapA promoter region and blocks the progression of the RNA polymerase, leading to the arrest of the transcription.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Expression of genes in the gapA operon encoding five enzymes for triose phosphate interconversion in Bacillus subtilis is negatively regulated by the Central glycolytic genes Regulator (CggR). CggR belongs to the large SorC/DeoR family of prokaryotic transcriptional regulators, characterized by an N-terminal DNA-binding domain and a large C-terminal effector-binding domain. When no glucose is present in growth media, CggR binds to its target DNA sequence and blocks the transcription of genes in the gapA operon. In the presence of glucose, binding of the known effector molecule fructose-1,6-bisphosphate abolishes this interaction. We have identified dihydroxyacetone phosphate, glucose-6-phosphate, and fructose-6-phosphate as additional CggR ligands that can bind to the effector-binding site. Crystal structures of C-CggR, the C-terminal effector-binding domain of CggR, both unliganded as well as in complex with the four ligands at resolutions between 1.65 and 1.80 A reveal unique ligand-specific structural changes in the binding site that affect the dimer interface. Binding affinities of these ligands were determined by isothermal titration calorimetry. Chemical cross-linking shows that CggR oligomerization is mediated through its effector-binding domain and that binding of the different ligands differentially affects the distribution of oligomers. Electrophoretic mobility shift assays (EMSAs) confirmed a destabilizing effect of FBP on the CggR/DNA complex and also showed similar effects for dihydroxyacetone phosphate. Our results suggest that CggR stability and function may be modulated by various effectors in a complex fashion.

Crystal structures of the effector-binding domain of repressor CggR from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates.,Rezacova P, Kozisek M, Moy SF, Sieglova I, Joachimiak A, Machius M, Otwinowski Z Mol Microbiol. 2008 Jun 10;. PMID:18554327^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Fillinger S, Boschi-Muller S, Azza S, Dervyn E, Branlant G, Aymerich S. Two glyceraldehyde-3-phosphate dehydrogenases with opposite physiological roles in a nonphotosynthetic bacterium. J Biol Chem. 2000 May 12;275(19):14031-7. PMID:10799476
↑ Doan T, Aymerich S. Regulation of the central glycolytic genes in Bacillus subtilis: binding of the repressor CggR to its single DNA target sequence is modulated by fructose-1,6-bisphosphate. Mol Microbiol. 2003 Mar;47(6):1709-21. PMID:12622823
↑ Chaix D, Ferguson ML, Atmanene C, Van Dorsselaer A, Sanglier-Cianferani S, Royer CA, Declerck N. Physical basis of the inducer-dependent cooperativity of the Central glycolytic genes Repressor/DNA complex. Nucleic Acids Res. 2010 Sep;38(17):5944-57. doi: 10.1093/nar/gkq334. Epub 2010, May 12. PMID:20462860 doi:http://dx.doi.org/10.1093/nar/gkq334
↑ Rezacova P, Kozisek M, Moy SF, Sieglova I, Joachimiak A, Machius M, Otwinowski Z. Crystal structures of the effector-binding domain of repressor CggR from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates. Mol Microbiol. 2008 Jun 10;. PMID:18554327 doi:MMI6318

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3bxe"

Categories: Bacillus subtilis | Large Structures | Otwinowski Z | Rezacova P

@@ Line 1: / Line 1: @@
 ==Crystal structure of effector binding domain of central glycolytic gene regulator (CggR) from Bacillus subtilis in complex with dihydroxyacetone phosphate==
-<StructureSection load='3bxe' size='340' side='right' caption='[[3bxe]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='3bxe' size='340' side='right'caption='[[3bxe]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3bxe]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BXE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3bxe]] 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=3BXE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BXE FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2okg|2okg]], [[3bxf|3bxf]], [[3bxg|3bxg]], [[3bxh|3bxh]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cggR, yvbQ, BSU33950 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=3bxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bxe OCA], [https://pdbe.org/3bxe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bxe RCSB], [https://www.ebi.ac.uk/pdbsum/3bxe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bxe ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bxe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bxe RCSB], [http://www.ebi.ac.uk/pdbsum/3bxe PDBsum]</span></td></tr>
+</table>
-<table>
+== Function ==
+[https://www.uniprot.org/uniprot/CGGR_BACSU CGGR_BACSU] In the absence of glucose, represses the transcription of the gapA operon, which encodes five key glycolytic enzymes. Binds specifically to the cggR-gapA promoter region and blocks the progression of the RNA polymerase, leading to the arrest of the transcription.<ref>PMID:10799476</ref> <ref>PMID:12622823</ref> <ref>PMID:20462860</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bx/3bxe_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bx/3bxe_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3bxe ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3bxe" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 34: / Line 37: @@
 </StructureSection>
 [[Category: Bacillus subtilis]]
-[[Category: Otwinowski, Z.]]
+[[Category: Large Structures]]
-[[Category: Rezacova, P.]]
+[[Category: Otwinowski Z]]
-[[Category: Catabolic repressor]]
+[[Category: Rezacova P]]
-[[Category: Deor family]]
-[[Category: Dna-binding]]
-[[Category: Effector binding domain]]
-[[Category: Gene regulation]]
-[[Category: Transcription regulation]]
-[[Category: Transcriptional regulator]]

3bxe

From Proteopedia

Current revision

Crystal structure of effector binding domain of central glycolytic gene regulator (CggR) from Bacillus subtilis in complex with dihydroxyacetone phosphate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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