2RDE

Crystal structure of VCA0042 complexed with c-di-GMP

Summary for 2RDE

• Entry DOI: 10.2210/pdb2rde/pdb
• Descriptor: Uncharacterized protein VCA0042, 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) (3 entities in total)
• Functional Keywords: c-di-gmp, vibrio cholerae, vca0042, structural genomics, psi-2, protein structure initiative, northeast structural genomics consortium, nesg, unknown function
• Biological source: Vibrio cholerae
• Total number of polymer chains: 2
• Total formula weight: 57873.74

Authors

Benach, J.,Swaminathan, S.S.,Tamayo, R.,Seetharaman, J.,Handelman, S.,Forouhar, F.,Neely, H.,Camilli, A.,Hunt, J.F.,Northeast Structural Genomics Consortium (NESG) (deposition date: 2007-09-22, release date: 2007-10-30, Last modification date: 2023-08-30)

Primary citation

Benach, J.,Swaminathan, S.S.,Tamayo, R.,Handelman, S.K.,Folta-Stogniew, E.,Ramos, J.E.,Forouhar, F.,Neely, H.,Seetharaman, J.,Camilli, A.,Hunt, J.F.
The structural basis of cyclic diguanylate signal transduction by PilZ domains.
Embo J., 26:5153-5166, 2007

PubMed Abstract: The second messenger cyclic diguanylate (c-di-GMP) controls the transition between motile and sessile growth in eubacteria, but little is known about the proteins that sense its concentration. Bioinformatics analyses suggested that PilZ domains bind c-di-GMP and allosterically modulate effector pathways. We have determined a 1.9 A crystal structure of c-di-GMP bound to VCA0042/PlzD, a PilZ domain-containing protein from Vibrio cholerae. Either this protein or another specific PilZ domain-containing protein is required for V. cholerae to efficiently infect mice. VCA0042/PlzD comprises a C-terminal PilZ domain plus an N-terminal domain with a similar beta-barrel fold. C-di-GMP contacts seven of the nine strongly conserved residues in the PilZ domain, including three in a seven-residue long N-terminal loop that undergoes a conformational switch as it wraps around c-di-GMP. This switch brings the PilZ domain into close apposition with the N-terminal domain, forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface. The very small size of the N-terminal conformational switch is likely to explain the facile evolutionary diversification of the PilZ domain.

PubMed: 18034161
DOI: 10.1038/sj.emboj.7601918

Experimental method

X-RAY DIFFRACTION (1.92 Å)