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. 2012 Feb 20;7(2):e31528. doi: 10.1371/journal.pone.0031528

Figure 5. Helix 1, helix 13, and presence or absence of supratrimeric oligomerization in OTC and PTC.

Figure 5

(A) Cartoon representation of helix 1 (in orange) and H13* of the adjacent subunit (in dark green) showing residues involved in the contacts between these helices. (B) Oligomeric structures of (from right to left): pfOTC (PDB file 1PVV), Pseudomonas aeruginosa OTC (1DXH), Lactobacillus hilgardii OTC (2W37), hOTC (2OTH) and E. faecalis truncated PTC. For each structure, the biological assembly is shown in the top part, with each basic trimer encircled in a broken line, focusing in the bottom part on the interactions of helix 1. In hOTC the surface of a subunit is shown in semitransparent representation and helix 1 in illustrated in cartoon form. The color code of the helices shown in the bottom part corresponds to that of the subunits involved in the interactions shown. (C) Sequence alignment of the C-terminal portions of OTCs of known 3-D structure and of representative known or putative PTCs (annotated as such in UniProt and NCBI Protein databases). Red lettering marks the PTC sequence signature identified in helix 13. Underlining marks experimentally observed (OTCs and E. faecalis PTC) or predicted (other PTCs) α-helices. Secondary structure was predicted with SOPMA (http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html). PDB files are the following for OTCs: human, 1OTH; Ovis aries, 1FB5; Coccidioides immitis, 3SDS; P. furiosus1PVV; Mycobacterium tuberculosis, 2I6U; Gloeobacter violaceus, 3GD5; Thermus thermophilus, 2EF0; Giardia lamblia, 3GRF; E. coli, I form, 2OTC; P. aeruginosa, 1DXH; L. hilgardii, 2W37; Thermotoga maritima, 1VLV; Campylobacter jejuni, 3TPF. For PTCs, UniProt or NCBI Protein database entries are the following: E. faecalis, Q837U7; Eggerthella lenta, C8WMM1; S. mutans, Q8DW19; L. monocytogenes, D2P024; Pediococcus pentosaceus, Q03HM9; L. hilgardii, C0XJB3; Vibrio sinaloensis, E8M734; Mycoplasma mycoides, Q6MSR6; Slackia heliotrinireducens, YP_003143629.1; Photobacterium profundum, YP_133569.1; Caulobacter sp., YP_001684585.1; Parvibaculum lavamentivorans, YP_001412420.1.