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The Crystal Structure of the Protein of Unknown Function VCA0042 from Vibrio cholerae O1 (1yln)
PilZ
Binding site (R136, R140, D162, S164, G167)
1YLN is a 1 chain structure of sequence from Vibrio cholerae o1. Full crystallographic information is available from OCA.
Solution NMR structure of Pseudomonas Aeruginosa protein PA4608. Northeast Structural Genomics target PaT7 (1ywu)
Publication Abstract from PubMed
PA4608 is a 125 residue protein from Pseudomonas aeruginosa with a recent identification as a PilZ domain and putative bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) adaptor protein that plays a role in bacterial second-messenger regulated processes. The nuclear magnetic resonance (NMR) structure of PA4608 has been determined and c-di-GMP binding has been confirmed by NMR titration studies. The monomeric core structure of PA4608 contains a six-stranded anti-parallel beta barrel flanked by three helices. Conserved surface residues among PA4608 homologs suggest the c-di-GMP binding site is at one end of the barrel and includes residues in the helices as well as in the unstructured N-terminus. Chemical shift changes in PA4608 resonances upon titration with c-di-GMP confirm binding. This evidence supports the hypothesis that proteins containing PilZ domains are the long-sought c-di-GMP adaptor proteins.
NMR structure and binding studies confirm that PA4608 from Pseudomonas aeruginosa is a PilZ domain and a c-di-GMP binding protein., Ramelot TA, Yee A, Cort JR, Semesi A, Arrowsmith CH, Kennedy MA, Proteins. 2007 Feb 1;66(2):266-71. PMID:17096419
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
Chain
C-di-GMP binding site
PilZ active site (R9, R13, D35, S37, G40)
Crystal structure of predicted glycosyltransferase from Pseudomonas putida KT2440 at 2.25 A resolution (2gjg)
PilZ domain
Binding sites (R123xxR, D157xSxxG)
Active sites (R123, R127, D157, S159, G162)
2GJG is a 1 chain structure of sequence from Pseudomonas putida. Full crystallographic information is available from OCA.
Crystal structure of VCA0042 complexed with c-di-GMP (2rde)
Pilz domain
PilZ
Binding sites (R136, R140, D162, S164, G167)
Binding sites + ligand
Active sites (R136, R140, D162, S164, G167)
Publication Abstract from PubMed
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.
The structural basis of cyclic diguanylate signal transduction by PilZ domains., Benach J, Swaminathan SS, Tamayo R, Handelman SK, Folta-Stogniew E, Ramos JE, Forouhar F, Neely H, Seetharaman J, Camilli A, Hunt JF, EMBO J. 2007 Dec 12;26(24):5153-66. Epub 2007 Nov 22. PMID:18034161
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
About this Structure
2RDE is a 2 chains structure of sequences from Vibrio cholerae o395. Full crystallographic information is available from OCA.
