On methylene‐bridged cysteine and lysine residues in proteins

Abstract

Cysteine residues ubiquitously stabilize tertiary and quaternary protein structure by formation of disulfide bridges. Here we investigate another linking interaction that involves sulfhydryl groups of cysteines, namely intra-and intermolecular methylene-bridges between cysteine and lysine residues. A number of crystal structures possessing such a linkage were identified in the Protein Data Bank. Inspection of the electron density maps and re-refinement of the nominated structures unequivocally confirmed the presence of Lys-CH 2 -Cys bonds in several cases.

Comment on Wang's paper on the covalent Cys‐X‐Lys bridges

“…Wang doubts our claim that the unexpected feature identified as a bridge between the side chains of Lys and Cys in the crystal structure of HPP and some other structures in the PDB is a methylene moiety. In his interpretation, these residues are connected by an O atom.…”

Crystallographic identification of spontaneous oxidation intermediates and products of protein sulfhydryl groups

“…Chemical methods have been developed for mapping the proteome landscape of sulfenylation and sulfinylation inside the cell . Therefore, it would be not surprising that crystal structures of many other proteins in the PDB also include oxidized Cys residues …”

“…Therefore, the formation of an O bridge between Cys and Lys residues is the most likely species to cross‐link the two side chains in many other proteins (even in the absence of supporting mass spectroscopic data), through a mechanism of oxidation of Cys residues followed by condensation. Given the widespread presence of this species in the PDB database, one has to wonder whether the O cross‐linking species is present inside the cell, and whether it performs some important cellular functions, which could easily escape from proteome mapping of cellular Cys oxidation.…”

“…1 Further systematic analysis of other proteins crystal structures in the PDB suggested that the presumed species might be widespread. 2 These results are rather unexpected because it is a spontaneous reaction to oxidize carbohydrates and CH 2 units by O 2 to generate CO 2 and H 2 O, but not its reverse reaction. The reverse reaction, i.e., the reduction of CO 2 to generate carbohydrates or CH 2 units and oxidation of H 2 O or CO 2 to generate O 2 , are the two most difficult redox reactions on the planet.…”

“…A recent crystallographic analysis suggested that side chains of Cys‐245 and Lys‐158 in histidinol phosphate phosphatase (HPP; PDB ID: 5EQA) could readily capture CO 2 and reduce it to CH 2 as a bridge between the two side chains based on the structure determined at 1.32‐Å resolution in combination with mass spectrometry . Further systematic analysis of other proteins crystal structures in the PDB suggested that the presumed species might be widespread . These results are rather unexpected because it is a spontaneous reaction to oxidize carbohydrates and CH 2 units by O 2 to generate CO 2 and H 2 O, but not its reverse reaction.…”