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| | <StructureSection load='5y6g' size='340' side='right'caption='[[5y6g]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='5y6g' size='340' side='right'caption='[[5y6g]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5y6g]] 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=5Y6G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y6G FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5y6g]] 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=5Y6G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y6G FirstGlance]. <br> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| - | <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>
| + | <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> |
| - | <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=5y6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6g OCA], [http://pdbe.org/5y6g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y6g RCSB], [http://www.ebi.ac.uk/pdbsum/5y6g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6g 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=5y6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6g OCA], [https://pdbe.org/5y6g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y6g RCSB], [https://www.ebi.ac.uk/pdbsum/5y6g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6g ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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> | + | [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> |
| | <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: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Hou, Y J]] | + | [[Category: Hou YJ]] |
| - | [[Category: Li, D F]] | + | [[Category: Li DF]] |
| - | [[Category: Wang, D C]] | + | [[Category: Wang DC]] |
| - | [[Category: C-di-gmp binding]]
| + | |
| - | [[Category: Flagellar brake protein]]
| + | |
| - | [[Category: Pilz domain]]
| + | |
| - | [[Category: Protein binding]]
| + | |
| Structural highlights
Function
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.[1] [2] [3] [4]
Publication Abstract from PubMed
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.
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[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ko M, Park C. Two novel flagellar components and H-NS are involved in the motor function of Escherichia coli. J Mol Biol. 2000 Oct 27;303(3):371-82. PMID:11031114 doi:http://dx.doi.org/10.1006/jmbi.2000.4147
- ↑ Ryjenkov DA, Simm R, Romling U, Gomelsky M. The PilZ domain is a receptor for the second messenger c-di-GMP: the PilZ domain protein YcgR controls motility in enterobacteria. J Biol Chem. 2006 Oct 13;281(41):30310-4. doi: 10.1074/jbc.C600179200. Epub 2006 , Aug 18. PMID:16920715 doi:http://dx.doi.org/10.1074/jbc.C600179200
- ↑ Boehm A, Kaiser M, Li H, Spangler C, Kasper CA, Ackermann M, Kaever V, Sourjik V, Roth V, Jenal U. Second messenger-mediated adjustment of bacterial swimming velocity. Cell. 2010 Apr 2;141(1):107-16. doi: 10.1016/j.cell.2010.01.018. Epub 2010 Mar, 18. PMID:20303158 doi:http://dx.doi.org/10.1016/j.cell.2010.01.018
- ↑ Paul K, Nieto V, Carlquist WC, Blair DF, Harshey RM. The c-di-GMP binding protein YcgR controls flagellar motor direction and speed to affect chemotaxis by a "backstop brake" mechanism. Mol Cell. 2010 Apr 9;38(1):128-39. doi: 10.1016/j.molcel.2010.03.001. Epub 2010, Mar 25. PMID:20346719 doi:10.1016/j.molcel.2010.03.001
- ↑ Hou YJ, Yang WS, Hong Y, Zhang Y, Wang DC, Li DF. Structural insights into the mechanism of c-di-GMP-bound YcgR regulating flagellar motility in Escherichia coli. J Biol Chem. 2020 Jan 17;295(3):808-821. doi: 10.1074/jbc.RA119.009739. Epub 2019, Dec 13. PMID:31836667 doi:http://dx.doi.org/10.1074/jbc.RA119.009739
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