3KYG

Crystal structure of VCA0042 (L135R) complexed with c-di-GMP

Summary for 3KYG

• Entry DOI: 10.2210/pdb3kyg/pdb
• Related: 3KYG
• Descriptor: Putative uncharacterized protein VCA0042, GUANOSINE-5'-MONOPHOSPHATE (3 entities in total)
• Functional Keywords: c-di-gmp, pilz domain, pp4397, vca0042, unknown function
• Biological source: Vibrio cholerae
• Cellular location: Bacterial flagellum basal body (Potential): Q9KNC3
• Total number of polymer chains: 2
• Total formula weight: 54254.88

Authors

Ryu, K.S.,Ko, J.,Kim, H.,Choi, B.S. (deposition date: 2009-12-06, release date: 2010-04-14, Last modification date: 2024-05-29)

Primary citation

Ko, J.,Ryu, K.S.,Kim, H.,Shin, J.S.,Lee, J.O.,Cheong, C.,Choi, B.S.
Structure of PP4397 Reveals the Molecular Basis for Different c-di-GMP Binding Modes by Pilz Domain Proteins.
J.Mol.Biol., 398:97-110, 2010

PubMed Abstract: Cyclic diguanylate (c-di-GMP) is a global regulator that modulates pathogen virulence and biofilm formation in bacteria. Although a bioinformatic study revealed that PilZ domain proteins are the long-sought c-di-GMP binding proteins, the mechanism by which c-di-GMP regulates them is uncertain. Pseudomonas putida PP4397 is one such protein that contains YcgR-N and PilZ domains and the apo-PP4397 structure was solved earlier by the Joint Center for Structural Genomics. We determined the crystal structure of holo-PP4397 and found that two intercalated c-di-GMPs fit into the junction of its YcgR-N and PilZ domains. Moreover, c-di-GMP binding induces PP4397 to undergo a dimer-to-monomer transition. Interestingly, another PilZ domain protein, VCA0042, binds to a single molecule of c-di-GMP, and both its apo and holo forms are dimeric. Mutational studies and the additional crystal structure of holo-VCA0042 (L135R) showed that the Arg122 residue of PP4397 is crucial for the recognition of two molecules of c-di-GMP. Thus, PilZ domain proteins exhibit different c-di-GMP binding stoichiometry and quaternary structure, and these differences are expected to play a role in generating diverse forms of c-di-GMP-mediated regulation.

PubMed: 20226196
DOI: 10.1016/j.jmb.2010.03.007

Experimental method

X-RAY DIFFRACTION (2.1 Å)