5Y6F

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

Summary for 5Y6F

• Entry DOI: 10.2210/pdb5y6f/pdb
• Descriptor: Flagellar brake protein YcgR, SULFATE ION, 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), ... (4 entities in total)
• Functional Keywords: c-di-gmp binding, flagellar brake protein, motor protein binding, pilz domain, protein binding
• Biological source: Escherichia coli (strain K12)
• Total number of polymer chains: 1
• Total formula weight: 30895.72

Authors

Hou, Y.J.,Wang, D.C.,Li, D.F. (deposition date: 2017-08-11, release date: 2018-07-18, Last modification date: 2024-03-27)

Primary citation

Hou, Y.J.,Yang, W.S.,Hong, Y.,Zhang, Y.,Wang, D.C.,Li, D.F.
Structural insights into the mechanism of c-di-GMP-bound YcgR regulating flagellar motility inEscherichia coli.
J.Biol.Chem., 295:808-821, 2020

PubMed Abstract: 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 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 RR motif and the C-tail helix α3. 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.

PubMed: 31836667
DOI: 10.1074/jbc.RA119.009739

Experimental method

X-RAY DIFFRACTION (2.3 Å)