tRNA-pseudouridine synthase II (TruB) from Thermotoga maritima catalyses the conversion of tRNA uridine to tRNA pseudouridine at position 55 in tRNA. The formation of pseudouridine is shown to be important for the structural integrity of tRNA.
TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA [PMID:11779468].
The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. [PMID:10529181]
There is still much debate as to the exact mechanism of this enzyme.
Defined by 4 residues: ASP:A-39TYR:A-67ASP:A-81ARG:A-172
