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5y6h

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Crystal structure of YcgR-N domain of YcgR from Escherichia coli

Structural highlights

5y6h is a 1 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.774Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5y6h"

@@ Line 3: / Line 3: @@
 <StructureSection load='5y6h' size='340' side='right'caption='[[5y6h]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5y6h]] 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=5Y6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y6H FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5y6h]] 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=5Y6H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y6H FirstGlance]. <br>
-</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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.774&#8491;</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=5y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6h OCA], [http://pdbe.org/5y6h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y6h RCSB], [http://www.ebi.ac.uk/pdbsum/5y6h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6h 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=5y6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y6h OCA], [https://pdbe.org/5y6h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y6h RCSB], [https://www.ebi.ac.uk/pdbsum/5y6h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y6h ProSAT]</span></td></tr>
 </table>
 == 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;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
 [[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: Yang, W S]]
+[[Category: Yang WS]]
-[[Category: Flagellar brake protein]]
-[[Category: Unknown function]]
-[[Category: Ycgr]]
-[[Category: Ycgr-n domain]]

5y6h

From Proteopedia

Current revision

Crystal structure of YcgR-N domain of YcgR from Escherichia coli

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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