CYTH-like domain superfamily (IPR033469)
Short name: CYTH-like_dom_sf
- mRNA triphosphatase Cet1-like (IPR004206)
- Adenylyl cyclase CyaB (IPR008173)
- Uncharacterised protein family YjbK (IPR009195)
- Inorganic triphosphatase NeuTTM/CthTTM-like (IPR012042)
- Uncharacterised protein family, CYTH/CHAD/HD-like domain-containing (IPR012069)
- Thiamine triphosphatase, eukaryotes (IPR012177)
- CYTH domain (IPR023577)
- Triphosphate tunel metalloenzyme 3 (IPR033245)
- mRNA triphosphatase Cet1-like superfamily (IPR037009)
- Inorganic triphosphatase YgiF (IPR039013)
- Thiamine-triphosphatase (IPR039582)
The bacterial CyaB like adenylyl cyclase and the mammalian thiamine triphosphatases (ThTPases) define a superfamily of catalytic domains called the CYTH (CyaB, thiamine triphosphatase) domain that is present in all three superkingdoms of life [PMID: 22984449]. Proteins containing this domain act on triphosphorylated substrates and require at least one divalent metal cation for catalysis [PMID: 24021036].
The catalytic core of the CYTH domain is predicted to contain an alpha+beta scaffold with 6 conserved beta-strands and 6 conserved alpha-helices. The CYTH domains contains several nearly universally conserved charged residues that are likely to form the active site. The most prominent of these are an EXEXK motif associated with strand-1 of the domain, two basic residues in helix-2, a K at the end of strand 3, an E in strand 4, a basic residue in helix-4, a D at the end of strand 5 and two acidic residues (typically glutamates) in strand 6. The presence of around 6 conserved acidic positions in the majority of the CYTH domains suggests that it coordinates two divalent metal ions. Both CyaB and ThTPase have been shown to require Mg(2+) ions for their nucleotide cyclase and phosphatase activities. The four conserved basic residues in the CYTH domain are most probably involved in the binding of acidic phosphate moieties of their substrates. The conservation of these two sets of residues in the majority of CYTH domains suggests that most members of this group are likely to possess an activity dependent on two metal ions, with a preference for nucleotides or related phosphate-moiety -bearing substrates. The proposed biochemical activity, and the arrangement of predicted strands in the primary structure of the CYTH domain imply that they may adopt a barrel or sandwich- like configuration, with metal ions and the substrates bound in the central cavity [PMID: 12456267].
Protein containing a CYTH-like domain include the yeast RNA triphosphatase Cet1, whose active site is located within a topologically closed hydrophilic beta-barrel (composed of 8 antiparallel beta strands) known as the "triphosphate tunnel" [PMID: 10589681]. Gong et al., gave the name - "Triphosphate Tunnel Metalloenzyme" (TTM), to this superfamily including Cet-1-like RNA triphosphatases and all other CYTH proteins [PMID: 16809816].
Interestingly, bacterial CYTH-domain containing proteins, such as NeuTTM (Q82UI9) from Nitrosomonas europaea [PMID: 21840996] and CthTTM (A3DIJ8) from Clostridium thermocellum [PMID: 17303560], both have a high PPPase activity (though CthTM was less specific) but neither had any significant adenylyl cyclase activity. However, other bacterial CYTH-domain containing proteins, such as CyaB from A. hydrophyla and ygiF from E. coli, have been shown to have PPPase activity, but this activity is lower than their adenylate cyclase activity [PMID: 22984449]. It has also been suggested that adenylyl cyclase and thiamine triphosphatase are secondary derivatives of proteins that performed an ancient role in polyphosphate and nucleotide metabolism [PMID: 12456267].
- SSF55154 (SSF55154)