Protein Family Models

This domain is found linked to a wide range of non-homologous domains in a variety of bacteria. It has been shown to be homologous to the adenylyl cyclase catalytic domain [1] and has diguanylate cyclase activity [4]. This observation correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. In the WspR protein of Pseudomonas aeruginosa, the GGDEF domain acts as a diguanylate cyclase, PDB:3bre, when the whole molecule appears to form a tetramer consisting of two symmetrically-related dimers representing a biological unit. The active site is the GGD/EF motif, buried in the structure, and the cyclic dimeric guanosine monophosphate (c-di-GMP) bind to the inhibitory-motif RxxD on the surface. The enzyme thus catalyses the cyclisation of two guanosine triphosphate (GTP) molecules to one c-di-GMP molecule [6,7,8]. [1]. 11119645. GGDEF domain is homologous to adenylyl cyclase. Pei J, Grishin NV;. Proteins 2001;42:210-216. [2]. 11557134. Novel domains of the prokaryotic two-component signal transduction systems. Galperin MY, Nikolskaya AN, Koonin EV;. FEMS Microbiol Lett 2001;203:11-21. [3]. 15063857. Cyclic di-guanosine-monophosphate comes of age: a novel secondary messenger involved in modulating cell surface structures in bacteria?. Jenal U;. Curr Opin Microbiol 2004;7:185-191. [4]. 15075296. Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain. Paul R, Weiser S, Amiot NC, Chan C, Sch. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-10-16

This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues. The EAL domain is a good candidate for a diguanylate phosphodiesterase function [1]. The domain contains many conserved acidic residues that could participate in metal binding and might form the phosphodiesterase active site [1]. [1]. 11557134. Novel domains of the prokaryotic two-component signal transduction systems. Galperin MY, Nikolskaya AN, Koonin EV;. FEMS Microbiol Lett 2001;203:11-21. (from Pfam)

Date:

2024-10-16

This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. This domain recognises Nicotinate, quidalnate, pyridine-2,5-dicarboxylate and salicylate [1]. [1]. 34424339. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. Matilla MA, Velando F, Martin-Mora D, Monteagudo-Cascales E, Krell T;. FEMS Microbiol Rev. 2022;46:fuab043. (from Pfam)

Date:

2024-10-16

The GGDEF domain is named for the motif GG[DE]EF shared by many proteins carrying the domain. There is evidence that the domain has diguanylate cyclase activity [1][3]. Several proteins carrying this domain also carry domains with functions relating to environmental sensing. These include PleD, a response regulator protein involved in the swarmer-to-stalked cell transition in Caulobacter crescentus[2], and FixL, a heme-containing oxygen sensor protein.

Date:

2021-04-27