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Since the closest homolog, with a solved structure, to the mycobacterial enzyme, was the E. coli CoaE, we modeled the NTD on the E. coli structure (32.7% identity, 54.7% similarity).
In addition, the location of the ring forming and other essential amino acids, i. e. the LanA1 motif, is conserved for the terminal three rings, indicating that the C-terminal ring structure of Licα might be identical to that of the other α-peptides with a solved structure (lacticin 3147 [41] and haloduracin [40]).
Unfortunately, we could not identify any homologous proteins with a solved crystal structure in extant databases (see Materials and Methods).
We compared docking performance to that of the empirical screen on a set of 20 HADSF members with a solved unliganded crystal structure (Table 1).
BLASTP searching of the PDB [ 34] showed that the closest homologue of hsENOSF1β and drENOSF1β with a solved structure and known biochemical activity is fuconate dehydratase (FucD, [PDB: 1YEY]) from the plant pathogenic bacteria Xanthomonas campestris [ 12].
Notably, all of the 33 enzymes with a solved 3-D structure have been assigned to a subfamily, resulting in thirteen individual subfamilies out of 51 with at least one structural representative.
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Phases were obtained by molecular replacement with a previously solved ubiquitin structure (PDB ID: 1UBQ) 20 as a search model.
There are 3 families of PyrD, each with a different solved quaternary structure [ 33].
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