Journal:Acta Cryst D:S2059798319000676
From Proteopedia
Crystal structures of pyrrolidone-carboxylate peptidase I from Deinococcus radiodurans reveal the mechanism of L-pyroglutamate recognitionRavindra Makde [1] Molecular Tour (spectrum color) is shown in cartoon with pG bound to the active site shown in magenta ball-and-sticks. Briefly, the monomeric structure of PCPdr consists of a single α/β fold in which a twisted seven-stranded mixed β-sheet (β1-β5, β8, and β9) is flanked by two α helices on one side (α2, and α4) and three α helices (α1, α3, and α6) on other side. The active site is entirely formed by residues from only one monomeric subunit. It is located at the depression which is formed by the protruding loops of the α/β core of the protein. These loops are which could play an important role in substrate entry. The residues of , are located at the N-terminus of helix α4, C-terminus of strand β5 and C-terminus of strand β11, respectively. Residues responsible for recognizing pG residue are mostly contributed by a flexible loop (loop-A), present near the active site. Phenylalanine residues of loop-A form stacking interactions with the pyrrolidone ring of pG, while Asn18 forms a hydrogen bond with OE of pG. These residues are conserved in all the known PCPs I, including those from mammals. The pG residue of peptides is recognized in the S1 substrate subsite of the enzyme by both van der Waals, and polar interactions, which provide specificity for the pG residue of the peptide.
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