6SFT

Solution structure of protein ARR_CleD in complex with c-di-GMP

Summary for 6SFT

• Entry DOI: 10.2210/pdb6sft/pdb
• NMR Information: BMRB: 27990,50001
• Descriptor: Two-component receiver protein CleD, 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) (2 entities in total)
• Functional Keywords: c-di-gmp, cled, chey, response regulator, signaling protein
• Biological source: Caulobacter vibrioides (strain NA1000 / CB15N)
• Total number of polymer chains: 1
• Total formula weight: 5555.51

Authors

Habazettl, J.,Hee, C.S.,Jenal, U.,Schirmer, T.,Grzesiek, S. (deposition date: 2019-08-02, release date: 2020-06-10, Last modification date: 2024-06-19)

Primary citation

Hee, C.S.,Habazettl, J.,Schmutz, C.,Schirmer, T.,Jenal, U.,Grzesiek, S.
Intercepting second-messenger signaling by rationally designed peptides sequestering c-di-GMP.
Proc.Natl.Acad.Sci.USA, 117:17211-17220, 2020

PubMed Abstract: The bacterial second messenger cyclic diguanylate (c-di-GMP) regulates a wide range of cellular functions from biofilm formation to growth and survival. Targeting a second-messenger network is challenging because the system involves a multitude of components with often overlapping functions. Here, we present a strategy to intercept c-di-GMP signaling pathways by directly targeting the second messenger. For this, we developed a c-di-GMP-sequestering peptide (CSP) that was derived from a CheY-like c-di-GMP effector protein. CSP binds c-di-GMP with submicromolar affinity. The elucidation of the CSP⋅c-di-GMP complex structure by NMR identified a linear c-di-GMP-binding motif, in which a self-intercalated c-di-GMP dimer is tightly bound by a network of H bonds and π-stacking interactions involving arginine and aromatic residues. Structure-based mutagenesis yielded a variant with considerably higher, low-nanomolar affinity, which subsequently was shortened to 19 residues with almost uncompromised affinity. We demonstrate that endogenously expressed CSP intercepts c-di-GMP signaling and effectively inhibits biofilm formation in , the most widely used model for serious biofilm-associated medical implications.

PubMed: 32611811
DOI: 10.1073/pnas.2001232117

Experimental method

SOLUTION NMR