diguanylate cyclase

Diguanylate cyclases are characterized by the conserved amino acid sequence motifs “GGDEF” (Gly-Gly-Asp-Glu-Phe) or “GGEEF” (Gly-Gly-Glu-Glu-Phe), which constitute the domain of the DGC active site.

{{cite journal | vauthors = Ausmees N, Mayer R, Weinhouse H, Volman G, Amikam D, Benziman M, Lindberg M | title = Genetic data indicate that proteins containing the GGDEF domain possess diguanylate cyclase activity | journal = FEMS Microbiology Letters | volume = 204 | issue = 1 | pages = 163–7 | date = October 2001 | pmid = 11682196 | doi = 10.1111/j.1574-6968.2001.tb10880.x | doi-access = free }} These domains are often found coupled to other signaling domains within multidomain proteins. Often, GGDEF domains with DGC activity are found in the same proteins as c-di-GMP-specific phosphodiesterase (PDE) EAL (Glu-Ala-Leu) domains.

{{cite journal | vauthors = Stock AM | title = Diguanylate cyclase activation: it takes two | journal = Structure | volume = 15 | issue = 8 | pages = 887–8 | date = August 2007 | pmid = 17697992 | doi = 10.1016/j.str.2007.07.003 | doi-access = free }}

{{cite journal | vauthors = Ryjenkov DA, Tarutina M, Moskvin OV, Gomelsky M | title = Cyclic diguanylate is a ubiquitous signaling molecule in bacteria: insights into biochemistry of the GGDEF protein domain | journal = Journal of Bacteriology | volume = 187 | issue = 5 | pages = 1792–8 | date = March 2005 | pmid = 15716451 | pmc = 1064016 | doi = 10.1128/JB.187.5.1792-1798.2005 }}

DGC is thought to only be active as a dimer consisting of two subunits, both with GGDEF domains.

{{cite journal | vauthors = Chan C, Paul R, Samoray D, Amiot NC, Giese B, Jenal U, Schirmer T | title = Structural basis of activity and allosteric control of diguanylate cyclase | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 101 | issue = 49 | pages = 17084–9 | date = December 2004 | pmid = 15569936 | pmc = 535365 | doi = 10.1073/pnas.0406134101 | doi-access = free }} The active (or catalytic) site is located at the interface between the two subunits, each binding one molecule of GTP. (See Activation mechanism and Regulation section for more information)

Weak sequence similarity and pronounced secondary structure similarity between GGDEF domains and the catalytic domains of adenylate cyclases (AC) have led to the hypothesis that DGCs and ACs share a similar fold.

{{cite journal | vauthors = Pei J, Grishin NV | title = GGDEF domain is homologous to adenylyl cyclase | journal = Proteins | volume = 42 | issue = 2 | pages = 210–6 | date = February 2001 | pmid = 11119645 | doi = 10.1002/1097-0134(20010201)42:2<210::AID-PROT80>3.0.CO;2-8 | s2cid = 13943884 }} This was verified with the resolution of the crystal structure of the DGC PleD from Caulobacter crescentus in complex with c-di-GMP. As shown in the figure, active PleD, shown as a dimer, is composed of the catalytic DCG domain (labeled DGC) and two CheY-like receiver domains (labeled D1/D2). The DGC domain of each subunit is linked to the two CheY-like domains by a flexible peptide linkage chain. The DCG domain closely resembles the domain of the AC catalytic core which consists of a five-stranded β-sheet surrounded by helices.

File:Pled Domains.png

As of mid-2011, 11 crystal structures of confirmed or putative DGCs have been solved, with PDB accession codes {{PDB|3N53}}, {{PDB|3N3T}}, {{PDB|3MTK}}, {{PDB|2WB4}}, {{PDB|3KZP}}, {{PDB|3HVA}}, {{PDB|3I5A}}, {{PDB|3IGN}}, {{PDB|3HVW}}, {{PDB|3H9W}}, and {{PDB|2R60}}.

Diguanylate cyclase participate in the formation of the ubiquitous second messenger, cyclic-di-GMP, involved in bacterial biofilm formation and persistence. The GGDEF domain was first identified in the regulatory protein, PleD of the bacterium Caulobacter crescentus.

{{cite journal | vauthors = Hecht GB, Newton A | title = Identification of a novel response regulator required for the swarmer-to-stalked-cell transition in Caulobacter crescentus | journal = Journal of Bacteriology | volume = 177 | issue = 21 | pages = 6223–9 | date = November 1995 | pmid = 7592388 | pmc = 177463 | doi = 10.1128/jb.177.21.6223-6229.1995}} It was later noted that numerous bacterial genomes encoded multiple proteins with a GGDEF domain.

{{cite journal | vauthors = Galperin MY, Nikolskaya AN, Koonin EV | title = Novel domains of the prokaryotic two-component signal transduction systems | journal = FEMS Microbiology Letters | volume = 203 | issue = 1 | pages = 11–21 | date = September 2001 | pmid = 11557134 | doi = 10.1016/S0378-1097(01)00326-3 | doi-access = free }} Pseudomonas aeruginosa PAO1 has 33 proteins with GGDEF domains, Escherichia coli K-12 has 19, and Vibrio cholerae O1 has 41.

{{cite journal | vauthors = D'Argenio DA, Miller SI | title = Cyclic di-GMP as a bacterial second messenger | journal = Microbiology | volume = 150 | issue = Pt 8 | pages = 2497–502 | date = August 2004 | pmid = 15289546 | doi = 10.1099/mic.0.27099-0 | doi-access = free }} In the cell cycle of Caulobacter crescentus, DGC PleD is known to control pole morphogenesis.

{{cite journal | vauthors = Aldridge P, Paul R, Goymer P, Rainey P, Jenal U | title = Role of the GGDEF regulator PleD in polar development of Caulobacter crescentus | journal = Molecular Microbiology | volume = 47 | issue = 6 | pages = 1695–708 | date = March 2003 | pmid = 12622822 | doi = 10.1046/j.1365-2958.2003.03401.x | doi-access = free }} In Pseudomonas fluorescens DGC WspR activity is hypothesized to be partially responsible for the wrinkly spreader (WS) phenotype.

{{cite journal | vauthors = Malone JG, Williams R, Christen M, Jenal U, Spiers AJ, Rainey PB | title = The structure-function relationship of WspR, a Pseudomonas fluorescens response regulator with a GGDEF output domain | journal = Microbiology | volume = 153 | issue = Pt 4 | pages = 980–94 | date = April 2007 | pmid = 17379708 | doi = 10.1099/mic.0.2006/002824-0 | doi-access = free }} In Pseudomonas aeruginosa, WspR has also been known to control autoaggregation.

During the cell cycle of C. crescentus, proteins with GGDEF and EAL domains are separated towards the two distinct poles. The active form of diguanylate cyclase PleD localizes to the stalked pole of differentiating C. crescentus cells.

{{cite journal | vauthors = Paul R, Weiser S, Amiot NC, Chan C, Schirmer T, Giese B, Jenal U | title = Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain | journal = Genes & Development | volume = 18 | issue = 6 | pages = 715–27 | date = March 2004 | pmid = 15075296 | pmc = 387245 | doi = 10.1101/gad.289504 }} It has been suggested that the function of PleD is two-fold. PleD is responsible for turning off flagellum rotations and inhibiting motility before genome replication begins and also for regenerating motility after differentiation has completed.

{{cite journal | vauthors = Skerker JM, Laub MT | title = Cell-cycle progression and the generation of asymmetry in Caulobacter crescentus | journal = Nature Reviews. Microbiology | volume = 2 | issue = 4 | pages = 325–37 | date = April 2004 | pmid = 15031731 | doi = 10.1038/nrmicro864 | s2cid = 41627093 }}

File:Activation Mechanism and Regulation of PleD.png

The crystal structure of the C. crescentus diguanylate cyclase, PleD, contains three domains; a GGDEF domain with diguanylate cyclase activity and two CheY-like receiver domains (D1/D2). As seen in the figure, the active form of PleD is a dimer which forms by phosphorylation of the first receiver domain (D1). Phosphorylation of the receiver domain increases the dimerization affinity by approximately 10-fold over non-phosphorylated domains.

{{cite journal | vauthors = Wassmann P, Chan C, Paul R, Beck A, Heerklotz H, Jenal U, Schirmer T | title = Structure of BeF3- -modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition | journal = Structure | volume = 15 | issue = 8 | pages = 915–27 | date = August 2007 | pmid = 17697997 | doi = 10.1016/j.str.2007.06.016 | doi-access = free }}

Inhibition of DGC activity is thought to be allosteric and non-competitive.

{{cite journal | vauthors = Paul R, Abel S, Wassmann P, Beck A, Heerklotz H, Jenal U | title = Activation of the diguanylate cyclase PleD by phosphorylation-mediated dimerization | journal = The Journal of Biological Chemistry | volume = 282 | issue = 40 | pages = 29170–7 | date = October 2007 | pmid = 17640875 | doi = 10.1074/jbc.M704702200 | doi-access = free }} Cyclic di-GMP binds to interface between the DGC and D2 domains stabilizing the open structure and preventing catalysis.

{{cite journal | vauthors = Christen B, Christen M, Paul R, Schmid F, Folcher M, Jenoe P, Meuwly M, Jenal U | title = Allosteric control of cyclic di-GMP signaling | journal = The Journal of Biological Chemistry | volume = 281 | issue = 42 | pages = 32015–24 | date = October 2006 | pmid = 16923812 | doi = 10.1074/jbc.M603589200 | doi-access = free }} Strong product inhibition has been observed with a Ki of 0.5 μM.

Though the exact catalytic mechanism has not been resolved, it is hypothesized that the dimerized structure of PleD facilitates interaction of the two GTP molecules within the DGC active site for cyclization. A proposed mechanism by Chan et al. indicates that the 3'-OH group of the GTP is deprotonated by a glutamic acid residue (E370) to allow for intermolecular nucleophilic attack of the α-phosphate. The pentacoordinated transition state created through this nucleophilic attack is possibly stabilized by a Lysine residue (K332).

File:C-di-GMP possible mechanism.png

{{reflist}}

{{refbegin}}

• {{cite journal | vauthors = Schirmer T, Jenal U | title = Structural and mechanistic determinants of c-di-GMP signalling | journal = Nature Reviews. Microbiology | volume = 7 | issue = 10 | pages = 724–35 | date = October 2009 | pmid = 19756011 | doi = 10.1038/nrmicro2203 | s2cid = 28824576 }}
• {{cite journal | vauthors = Jenal U, Malone J | title = Mechanisms of cyclic-di-GMP signaling in bacteria | journal = Annual Review of Genetics | volume = 40 | pages = 385–407 | year = 2006 | pmid = 16895465 | doi = 10.1146/annurev.genet.40.110405.090423 }}
• {{cite journal | vauthors = Hengge R | title = Principles of c-di-GMP signalling in bacteria | journal = Nature Reviews. Microbiology | volume = 7 | issue = 4 | pages = 263–73 | date = April 2009 | pmid = 19287449 | doi = 10.1038/nrmicro2109 | s2cid = 1937789 }}

{{refend}}

{{Kinases}}

{{Use dmy dates|date=April 2017}}

{{DEFAULTSORT:Diguanylate Cyclase}}

Category:EC 2.7.7