From sequence to structure to function: a case study

We have developed a WWW server for the rapid structural analysis of protein sequence/structure alignments. Users can submit an amino acid sequence to perform structural predictions and fold recognition. Pairwise 1D/3D alignments are then visualized as colored alignments to highlight sequence similarities and the relative positions of secondary structure elements and insertions/deletions. A pseudo-energy score is computed for each block in the proposed structural alignment to help manual refinement of the threading if necessary. Modelling is then performed using MODELLER and directly validated using Verify3D. The Web interfaces, we have developed, allow rapid and automatic molecular modelling even in the case of low sequence identity level (20–30%). Here, we report a structural analysis of the Thymidine Monophosphate Kinase (TMPK) from Campylobacter jejuni (hereafter, TMPKcj), a Gram-negative bacterium responsible for human diarrhea. Limited but significant sequence similarities could be detected with other nucleotide monophosphate kinases. The comparison of the TMPK with the crystal structure of other TMPK, strongly suggested that it might adopt a similar fold and revealed the conservation of the monomer-monomer interface. We propose a structural model of TMPKcj and analyze the slight differences at the levels of primary and 3D-structure suggesting putative variations in the binding of substrate analogs.