3kyf | pdb_00003kyf

Crystal structure of P4397 complexed with c-di-GMP

spinqualitylabelsall models 3kyf, resolution 2.10Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3kyf is a 1 chain structure with sequence from Pseudomonas putida. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: 5GP Related: 3kyg Gene: PP4397 (Pseudomonas putida) Resources: FirstGlance, OCA, RCSB, PDBsum Function [Q88EQ6_PSEPK] Acts as a flagellar brake, regulating swimming and swarming in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)-dependent manner. Increasing levels of c-di-GMP lead to decreased motility (By similarity). Binds c-di-GMP with a dissociation constant of 165 nM.[HAMAP-Rule:MF_01457] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. Structure of PP4397 reveals the molecular basis for different c-di-GMP binding modes by Pilz domain proteins.,Ko J, Ryu KS, Kim H, Shin JS, Lee JO, Cheong C, Choi BS J Mol Biol. 2010 Apr 23;398(1):97-110. Epub 2010 Mar 10. PMID:20226196 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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