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A Specialized Version of the HD Hydrolase Domain Implicated in Signal Transduction

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A Specialized Version of the HD Hydrolase Domain Implicated in Signal Transduction J. Mol. Microbiol. Biotechnol. (1999) 1(2): 303-305. The HD HydrolaseJMMB Domain in Correspondence Signal Transduction 303 A Specialized Version of the HD Hydrolase Domain Implicated in Signal Transduction Michael Y. Galperin*, Darren A. Natale, L. Aravind, extracytoplasmic ligand-binding domain and a cytoplas- and Eugene V. Koonin mic HD-GYP domain, connected by a transmembrane segment, has the same topology as methyl-accepting pro- National Center for Biotechnology Information, teins and many sensor kinases, which further supports the National Library of Medicine, National Institutes of Health, participation of the HD-GYP domain in signal transduc- Bethesda, Maryland 20894, USA tion. Finally, in the Aq_2027 protein from A. aeolicus, the HD-GYP domain is found together with the GGDEF do- main (Figure 2). The latter domain has been recently iden- Recently, a superfamily of proteins containing a previously tified in diguanylate cyclases and phosphodiesterases in- undetected domain with predicted metal-dependent volved in the regulation of cellulose synthesis in phosphohydrolase activity has been described and desig- Acetobacter xylinum (Tal et al., 1998) and in a variety of nated the HD superfamily, after the principal conserved bacterial signalling proteins in combination with CheY, PAS, residues implicated in catalysis (Aravind and Koonin, 1998). and HAMP domains (Hecht and Newton, 1995; Aravind In the course of our analysis of ancient conserved regions and Ponting, 1999). The GGDEF domain is often associ- in microbial genomes (Koonin et al., 1998), we found a ated with another uncharacterized domain, EAL, in par- distinct version of this domain which is encoded in one to ticular, in diguanylate cyclases and phosphodiesterases three copies in the genomes of Aquifex aeolicus, Borrelia (Tal et al., 1998; Aravind and Ponting, 1999). Remarkably, burgdorferi, Synechocystis sp. and Treponema pallidum, however, the combination of the HD-GYP and EAL domains but is dramatically expanded in the genomes of is not seen in any of the currently available microbial Thermotoga maritima and Clostridium acetobutylicum (Fig- genomes. Moreover, the number of copies of the HD-GYP ure 1). Compared with the consensus HD domain (Aravind domain in complete genomes generally correlates with and Koonin, 1998), this version contains a number of ad- prevalence of the GGDEF domain over the EAL domain ditional highly conserved residues; hereinafter we refer to (Table 1). Furthermore, the HD-GYP family of HD proteins it as the HD-GYP domain, after the characteristic sequence so far is lacking in archaea and eukaryotes and so are the signatures (Figure 1). This domain was also detected in GGDEF and EAL domains. This suggests that HD-GYP previously uncharacterized proteins from Wolinella domain might be also involved in cyclic diguanylate-medi- succinogenes (Kreis-Kleinschmidt et al., 1995), Bacillus ated signaling. The HD superfamily is related to the cAMP/ halodurans (Takami et al., 1999), Pseudomonas cGMP phosphodiesterases that are involved in eukaryotic aeruginosa and Bordetella pertussis (Figure 1). The HD- signalling (Aravind and Koonin, 1998). Therefore is seems GYP domain is missing in E. coli and B. subtilis. Remark- plausible that the HD-GYP family proteins are likely to pos- ably, however, in other γ-proteobacteria, such as sess a diguanylate phosphodiesterase activity and com- Shewanella putrefaciens and Vibrio cholerae, it is present plement the function that, in the characterized diguanylate in up to 8 copies (data not shown). phosphodiesterases, is performed by the EAL domain. While none of the proteins that contain the HD-GYP domain has ever been characterized experimentally, the spectrum of the domains that are associated with HD-GYP in multidomain proteins (Figure 2) suggests that it is prob- Table 1. Distribution of Three Domains Implicated in Signal Transduction in ably involved in signal transduction. In Synechocystis sp., Complete Microbial Genomes both copies of the HD-GYP domain are found in proteins that also contain CheY-like receiver domains of the two- Speciesa Domains component signal transduction system (Pao and Saier, GGDEF EAL HD-GYP 1995; Volz and Matsumura, 1991). A similar CheY – HD- GYP domain organization is found in two T. maritima pro- Escherichia coli 19 18 - teins, TM0186 and TM1147 (Figure 2). Two other proteins Rickettsia prowazekii 11- from T. maritima, TM1170 and TM1682, combine the HD- Bacillus subtilis 42- Mycobacterium tuberculosis 12- GYP domain with extracytoplasmic ligand-binding domains, Synechocystis sp. 23 13 2 which are closely related, respectively, to periplasmic sol- Borellia burgdorferi 111 ute-binding protein components of the ATP-dependent Treponema pallidum 1- 3 transport systems (Tam and Saier, 1993) and the Aquifex aeolicus 11 6 1 Thermotoga maritima 9- 9 extracytoplasmic part of methyl-accepting chemotaxis pro- Clostridium acetobutylicumb 10 4 8 teins of Bacillus subtilis, such as McpA and McpB (Hanlon and Ordal, 1994). Such a combination of an a Genomes of bacteria Haemophilus influenzae, Helicobacter pylori, Chlamy- dia trachomatis, C. pneumoniae, Mycoplasma genitalium, M. pneumoniae, and archaea Methanococcus jannaschii, Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, Pyrococcus horikoshii, and Received October 4, 1999; accepted October 4, 1999. Aeropyrum pernix do not contain any of these domains. *For correspondence. Email [email protected]; Tel. 301-435-5910; bPreliminary data based on unfinished genome sequence (http:// Fax. 301-480-9241. www.cric.com/sequence_center/bacterial_genomes) © 1999 Horizon Scientific Press Further Reading Caister Academic Press is a leading academic publisher of advanced texts in microbiology, molecular biology and medical research. 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The proteins are listed under their names in complete genomes (left column) and their unique gene identification (gi) numbers in the GenBank protein database (right column); the numbers indicate positions of the first and the last residues in each
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