Protein Family Models

This entry represents the second palm domain of Cas10 subunit (named Csm1 in Type III-A and Cmr2 in III-B systems) from type III CRISPR-Cas systems [6]. This domain contains a conserved GGDD motif that is important for DNA polymerase activity [1-5]. Paper describing PDB structure 3ung. [1]. 22405013. Structure of the Cmr2 subunit of the CRISPR-Cas RNA silencing complex. Cocozaki AI, Ramia NF, Shao Y, Hale CR, Terns RM, Terns MP, Li H;. Structure. 2012;20:545-553. Paper describing PDB structure 3w2v. [2]. 23583914. Crystal structure of the Cmr2-Cmr3 subcomplex in the CRISPR-Cas RNA silencing effector complex. Osawa T, Inanaga H, Numata T;. J Mol Biol. 2013;425:3811-3823. Paper describing PDB structure 4doz. [3]. 22449983. Crystal structure of Cmr2 suggests a nucleotide cyclase-related enzyme in type III CRISPR-Cas systems. Zhu X, Ye K;. FEBS Lett. 2012;586:939-945. Paper describing PDB structure 4h4k. [4]. 23395183. Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA silencing complex. Shao Y, Cocozaki AI, Ramia NF, Terns RM, Terns MP, Li H;. Structure. 2013;21:376-384. Paper describing PDB structure 4uw2. [5]. 25773141. Crystal structure of the Csm1 subunit of the Csm complex and its single-stranded DNA-specific nuclease activity. Jung TY, An Y, Park KH, Lee MH, Oh BH, Woo E;. Structure. 2015;23:782-790. [6]. 33352158. Mycobacterium tuberculosis CRISPR/Cas system Csm1 holds clues to the evolutionary relationship between DNA polymerase and cyclase activity. Zhang S, Li T, Huo Y, Yang J, Fleming J, Shi M, Wang Y, Wei W, Gu S, Bi L, Jiang T, Zhang H;. Int J Biol Macromol. 2021;170:140-149. (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

GGDEF domain-containing protein may have diguanylate cyclase (DGC) activity, similar to Escherichia coli DgcT (YcdT) and to E. coli CdgI (YeaI), a c-di-GMP-binding effector with a degenerate GGDEF domain which binds c-di-GMP

Date:

2024-04-21

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