Protein Family Models

PAS domains are involved in many signalling proteins where they are used as a signal sensor domain [1]. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Heme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. This domain recognises oxygen and CO (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 10357859. PAS domains: internal sensors of oxygen, redox potential, and. light.. Taylor BL, Zhulin IB;. Microbiol Mol Biol Rev. 1999;63:479-506. (from Pfam)

Date:

2024-07-13

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:

2024-07-15

This domain is found in many signalling proteins in which it functions as a sensor domain. It recognises FMN, Zn(II), FAD and riboflavin (MAtilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). (from Pfam)

Date:

2024-07-13

The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain is associated to signalling systems and works as a signal sensor domain. It recognises differently substituted aromatic hydrocarbons, oxygen, different dodecanoic acids, autoinducers, 3,5-dimethyl-pyrazin-2-ol and N-alanyl-aminoacetone (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 9301332. PAS domain S-boxes in archaea, bacteria and sensors for oxygen. and redox.. Zhulin IB, Taylor BL, Dixon R;. Trends Biochem Sci 1997;22:331-333.. [2]. 7756254. 1.4 A structure of photoactive yellow protein, a cytosolic. photoreceptor: unusual fold, active site, and chromophore.. Borgstahl GE, Williams DR, Getzoff ED;. Biochemistry 1995;34:6278-6287.. [3]. 9382818. PAS: a multifunctional domain family comes to light.. Ponting CP, Aravind L;. Curr Biol 1997;7:674-677.. [4]. 15009198. The PAS fold: a redefination of the PAS domain based upon. structural prediction.. Hefti MH, Francoijs KJ, de Vries SC, Dixon R, Vervoort J;. Eur J Biochem 2004;271:1198-1208. (from Pfam)

Date:

2024-07-13

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:

2024-07-10

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:

2024-07-09

The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). [1]. 9301332. PAS domain S-boxes in archaea, bacteria and sensors for oxygen. and redox.. Zhulin IB, Taylor BL, Dixon R;. Trends Biochem Sci 1997;22:331-333.. [2]. 7756254. 1.4 A structure of photoactive yellow protein, a cytosolic. photoreceptor: unusual fold, active site, and chromophore.. Borgstahl GE, Williams DR, Getzoff ED;. Biochemistry 1995;34:6278-6287.. [3]. 9382818. PAS: a multifunctional domain family comes to light.. Ponting CP, Aravind L;. Curr Biol 1997;7:674-677.. [4]. 15009198. The PAS fold: a redefination of the PAS domain based upon. structural prediction.. Hefti MH, Francoijs KJ, de Vries SC, Dixon R, Vervoort J;. Eur J Biochem 2004;271:1198-1208. (from Pfam)

Date:

2024-07-09