2RDE: Crystal Structure Of Vca0042 Complexed With C-di-gmp

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.
PDB ID: 2RDEDownload
MMDB ID: 60302
PDB Deposition Date: 2007/9/22
Updated in MMDB: 2007/12
Experimental Method:
x-ray diffraction
Resolution: 1.92  Å
Source Organism:
Similar Structures:
Biological Unit for 2RDE: dimeric; determined by author and by software (PISA)
Molecular Components in 2RDE
Label Count Molecule
Proteins (2 molecules)
Uncharacterized Protein Vca0042
Molecule annotation
Chemicals (2 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB