Protein Family Models

HD domains are metal dependent phosphohydrolases [1,2]. This entry covers the HD-GYP domain [2]. [1]. 9868367. The HD domain defines a new superfamily of metal-dependent. phosphohydrolases.. Aravind L, Koonin EV;. Trends Biochem Sci 1998;23:469-472.. [2]. 34928179. Sequence Conservation, Domain Architectures, and Phylogenetic. Distribution of the HD-GYP Type c-di-GMP Phosphodiesterases.. Galperin MY, Chou SH;. J Bacteriol. 2021; [Epub ahead of print] (from Pfam)

Date:

2024-08-14

The FIST C domain is a novel sensory domain, which is present in signal transduction proteins from Bacteria, Archaea and Eukarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids [1]. [1]. 17855421. FIST: a sensory domain for diverse signal transduction pathways. in prokaryotes and ubiquitin signaling in eukaryotes.. Borziak K, Zhulin IB;. Bioinformatics. 2007;23:2518-2521. (from Pfam)

Date:

2024-08-14

The FIST N domain is a novel sensory domain, which is present in signal transduction proteins from Bacteria, Archaea and Eukarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids [1]. [1]. 17855421. FIST: a sensory domain for diverse signal transduction pathways. in prokaryotes and ubiquitin signaling in eukaryotes.. Borziak K, Zhulin IB;. Bioinformatics. 2007;23:2518-2521. (from Pfam)

Date:

2024-08-14

HD domains are metal dependent phosphohydrolases. [1]. 9868367. The HD domain defines a new superfamily of metal-dependent. phosphohydrolases.. Aravind L, Koonin EV;. Trends Biochem Sci 1998;23:469-472. (from Pfam)

Date:

2024-08-14

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,. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

This domain is found in a few known nucleotidyltransferes and in a large number of uncharacterized proteins. It contains four widely separated His residues, the second of which is part of an invariant dipeptide His-Asp in a region matched approximately by the motif HDIG. For proteins scoring above the trusted cutoff, confidence is high both that the domain is present and that the HMM produces an essentially correct alignment. Protein regions scoring between the trusted and noise cutoffs include correctly aligned domains, homologous domains in which one or more of the His residues is conserved but misaligned, and some probable false-positive hits indications of homology.

Date:

2024-01-02

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