Homology-based models of a) “lid-open” and b) “lid-closed” conformations of Colias PEPCK. Models represent the cytosol form of allele Ser 335 – Glu 503 – Ile 629 (SEI). Ribbon model color code: green, β-strands; yellow, α-helices; red, loops. Space-filling model color code: red, substrates bound into catalytic center in b); dark blue, mobile lid loop; orange, polymorphic amino acid sites 335, 503, and 629 (standard numbering) which are shared between species; light blue, invariant amino acid sites Arg 272, Asp 334, Arg 506, and Leu 596. Note changes from structure a) with lid closure in structure b): separation of side chains of Asp 334 and Ser 335 with loss of hydrogen bond (cf. Figure 6); movement of Glu 503 to the right, and Arg 272 down, relative to Arg 506, forming 503–506 salt bridge (cf. Figure 7); loss of strong van der Waals contact between Leu 596 and Ile 629; shortening of the left end of the α-helix containing Leu 596.
Watt et al. BMC Evolutionary Biology 2013 13:9 doi:10.1186/1471-2148-13-9