5y6f

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<StructureSection load='5y6f' size='340' side='right'caption='[[5y6f]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='5y6f' size='340' side='right'caption='[[5y6f]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5y6f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y6F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y6F FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5y6f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y6F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y6F FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ycgR, b1194, JW1183 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5y6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6f OCA], [http://pdbe.org/5y6f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y6f RCSB], [http://www.ebi.ac.uk/pdbsum/5y6f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6f ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5y6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6f OCA], [https://pdbe.org/5y6f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y6f RCSB], [https://www.ebi.ac.uk/pdbsum/5y6f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6f ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/YCGR_ECOLI YCGR_ECOLI]] Acts as a flagellar brake, regulating swimming and swarming in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)-dependent manner. When bound to c-di-GMP it binds to elements of the flagellar motor (MotA (PubMed:20303158) and/or FliG and FliM (PubMed:20346719), binding to FliM also occurs in the absence of c-di-GMP), causing the motor to slow down. Thus, increasing levels of c-di-GMP lead to decreased motility. Probably binds 1 c-di-GMP dimer per subunit.<ref>PMID:11031114</ref> <ref>PMID:16920715</ref> <ref>PMID:20303158</ref> <ref>PMID:20346719</ref>
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[https://www.uniprot.org/uniprot/YCGR_ECOLI YCGR_ECOLI] Acts as a flagellar brake, regulating swimming and swarming in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)-dependent manner. When bound to c-di-GMP it binds to elements of the flagellar motor (MotA (PubMed:20303158) and/or FliG and FliM (PubMed:20346719), binding to FliM also occurs in the absence of c-di-GMP), causing the motor to slow down. Thus, increasing levels of c-di-GMP lead to decreased motility. Probably binds 1 c-di-GMP dimer per subunit.<ref>PMID:11031114</ref> <ref>PMID:16920715</ref> <ref>PMID:20303158</ref> <ref>PMID:20346719</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The motile-sessile transition is critical for bacterial survival and growth. Cyclic-di-GMP (c-di-GMP) plays a central role in controlling this transition and regulating biofilm formation via various effectors. As an effector of c-di-GMP in Escherichia coli and related species, the PilZ domain-containing protein YcgR responds to elevated c-di-GMP concentrations and acts on the flagellar motor to suppress bacterial motility in a brakelike fashion, which promotes bacterial surface attachment. To date, several target proteins within the motor, MotA, FliG, and FliM, along with different regulatory mechanisms have been reported. However, how YcgR acts on these components remains unclear. Here, we report that activated YcgR stably binds to MotA at the MotA-FliG interface and thereby regulates bacterial swimming. Biochemical and structural analyses revealed that c-di-GMP rearranges the PilZ domain configuration, resulting in the formation of a MotA-binding patch consisting of an RXXXR motif and the C-tail helix alpha3. Moreover, we noted that a conserved region in the YcgR-N domain, which is independent of MotA interaction, is necessary for motility regulation. On the basis of these findings, we infer that the YcgR-N domain is required for activity on other motor proteins. We propose that activated YcgR appends to MotA via its PilZ domain and thereby interrupts the MotA-FliG interaction and simultaneously interacts with other motor proteins via its YcgR-N domain to inhibit flagellar motility. Our findings suggest that the mode of interaction between YcgR and motor proteins may be shared by other PilZ family proteins.
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Structural insights into the mechanism of c-di-GMP-bound YcgR regulating flagellar motility in Escherichia coli.,Hou YJ, Yang WS, Hong Y, Zhang Y, Wang DC, Li DF J Biol Chem. 2020 Jan 17;295(3):808-821. doi: 10.1074/jbc.RA119.009739. Epub 2019, Dec 13. PMID:31836667<ref>PMID:31836667</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5y6f" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Ecoli]]
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[[Category: Escherichia coli K-12]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Hou, Y J]]
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[[Category: Hou YJ]]
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[[Category: Li, D F]]
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[[Category: Li DF]]
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[[Category: Wang, D C]]
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[[Category: Wang DC]]
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[[Category: C-di-gmp binding]]
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[[Category: Flagellar brake protein]]
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[[Category: Motor protein binding]]
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[[Category: Pilz domain]]
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[[Category: Protein binding]]
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Current revision

Crystal structure of YcgR in complex with c-di-GMP from Escherichia coli

PDB ID 5y6f

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Proteopedia Page Contributors and Editors (what is this?)

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