Protein Family Models

This entry represents the middle (Mid) domain of DosC proteins an oxygen-regulated diguanylate cyclase [1]. Paper describing PDB structure 4zvc. [1]. 26527135. Structural analysis of an oxygen-regulated diguanylate cyclase. Tarnawski M, Barends TR, Schlichting I;. Acta Crystallogr D Biol Crystallogr. 2015;71:2158-2177. (from Pfam)

Date:

2024-10-16

This family includes protoglobin from Methanosarcina acetivorans C2A. It is also found near the N-terminus of the Haem-based aerotactic transducer HemAT in Bacillus subtilis (Swiss:O07621). It is part of the haemoglobin superfamily. Protoglobin has specific loops and an amino-terminal extension which leads to the burying of the haem within the matrix of the protein. Protoglobin-specific apolar tunnels allow the access of O2, CO and NO to the haem distal site [1]. In HemAT it acts as an oxygen sensor domain [2]. It can also recognise cyanide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 18188182. Archaeal protoglobin structure indicates new ligand diffusion paths and modulation of haem-reactivity. Nardini M, Pesce A, Thijs L, Saito JA, Dewilde S, Alam M, Ascenzi P, Coletta M, Ciaccio C, Moens L, Bolognesi M;. EMBO Rep. 2008;9:157-163. [2]. 12962628. Structure of the oxygen sensor in Bacillus subtilis: signal transduction of chemotaxis by control of symmetry. Zhang W, Phillips GN Jr;. Structure. 2003;11:1097-1110. (from Pfam)

Date:

2024-10-16

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

diguanylate cyclase similar to DosC, an oxygen-sensing enzyme that catalyzes the synthesis of cyclic diguanylate (c-di-GMP) via the condensation of 2 GTP molecules

Date:

2022-10-14

Gene:

dosC

Date:

2020-04-18

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