Journal:Acta Cryst D:S2059798319000676

Crystal structures of pyrrolidone-carboxylate peptidase I from Deinococcus radiodurans reveal the mechanism of L-pyroglutamate recognition

Ravindra Makde ^[1]

Molecular Tour
L-pyroglutamate (pG) is formed by the cyclization of the side chain of glutamate or glutamine amino acid with alpha-amino group at the N-terminus of a polypeptide. This modified residue (pG) cannot be removed by any of the conventional peptidases. Special type of aminopeptidases called pyrrolidone-carboxylate peptidases (PCPs) (EC 3.4.19.-) can remove this unusual amino acid from the peptides or proteins. PCPs are of two types, a) PCPs I, which are cysteine peptidases of C15 family, b) PCPs II are metallopeptidases of M1 family. PCP I is highly conserved enzyme and its homologs have been found from bacteria to human. Many of the physiologically important peptide hormones (TRH, LHRH, GnRH) and antibodies have been shown to possess the pG residue at their N-termini. It seems to have implications in functional regulation of different peptides in both prokaryotes and eukaryotes. However, how these class of enzymes specifically catalyse the removal of pG residue remains mostly unknown. The crystal structures of PCP I from Deinococcus radiodurans (PCPdr) in its pG-free (PDB entry 5z47) and pG-bound (PDB entry 5z48) forms at high resolutions has helped to solve this puzzle.

. Each monomer is shown in different color. Bound substrate is shown in magenta spacefill representation. This tetrameric structure is similar to those observed in other PCP I proteins and buries equivalent surfaces of monomers for the formations of the tetramers.

(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.

. Water molecules are shown as red spheres. The presence of pG in the active site identifies the structural features that enable this enzyme to be a pG specific peptidase. pG is bound into a pocket formed by both hydrophobic and polar residues, Phe9, Phe12, Asn18, Val45, Gly70, Leu71, Tyr142, Val143, Cys144 and His169. The play a particularly important role in the pG binding. The while the . These residues are conserved in all the known PCPs I, including those from mammals. The residues from other loops also contribute significantly towards pG binding. The , respectively. The adjacent residue, , forms van der Waals contacts with OE of pG. Other van der Waals contacts for the pG binding are formed by the side chains of . The 5' carboxylate group of pG is held by several ionic interactions: while the . This water molecule is further stabilized by its interactions with the residues Tyr142, Asn145, and Ala139.

. PCPdr (present study; PDB entry 5z47; gray); Thermus thermophlius (PDB entry 2ebj; orange); Pyrococcus furiosus (PDB entry 2df5; violet); Thermococcus litoralis (PDB entry 1a2z; marine blue); Pyrococcus horikoshii (PDB entry 1iu8; yellow); Bacillus amyloliquefaciens (PDB entry 1aug; lime green); Bacillus anthrasis (PDB entry 3lac; chocolate); Xenorhabdus bovienii (PDB entry 4gxh; brown) and Staphylococcus aureus (PDB entry 3giu; cyan). (Value in the bracket is reference of Bacillus amyloliquefaciens).

PDB references: Crystal structure of pyrrolidone carboxylate peptidase I with disordered loop A from Deinococcus radiodurans R1 5z47; Crystal structure of pyrrolidone carboxylate peptidase I from Deinococcus radiodurans R1 bound to pyroglutamate 5z48.

References

1. ↑ Agrawal R, Singh R, Kumar A, Kumar A, Makde RD. Crystal structures of pyrrolidone-carboxylate peptidase I from Deinococcus radiodurans reveal the mechanism of L-pyroglutamate recognition. Acta Crystallogr D Struct Biol. 2019 Mar 1;75(Pt 3):308-316. doi:, 10.1107/S2059798319000676. Epub 2019 Feb 28. PMID:30950401 doi:http://dx.doi.org/10.1107/S2059798319000676