An SRLLR motif downstream of the scissile bond enhances enterokinase cleavage efficiency

In a previous paper, we reported more efficient enterokinase cleavage at a C-terminal non-target LKGDR201 site compared with an internally sited canonical recognition site, DDDDK156. When this non-target site was placed internally to replace DDDDK156 between the thioredoxin moiety and mouse NT-proCNP(1–50), this site was poorly processed leading us to conclude that efficient processing at LKGDR201 in the first instance was due to its accessibility at the C-terminus of the fusion protein. Subsequently, we reasoned that treatment of thioredoxin-fused NT-proCNP(1–81) would allow us to retrieve full-length NT-proCNP(1–81) without undue processing at the LKGDR201 site since this non-target site would now be located internally about 36 residues away from the C-terminus and hence not be hydrolyzed efficiently. Surprisingly, ESI-MS data showed that the LKGDR site in thioredoxin-fused human NT-proCNP(1–81) was still very efficiently cleaved and revealed a new but slow hydrolysis site with the sequence RVDTK↓SRAAW to yield a peptide consistent with NT-proCNP(58–81). The evidence obtained from these experiments led us to postulate that efficient cleavage at the non-target LKGDR201 site was not merely influenced by steric constraints but also by the sequence context downstream of the scissile bond. Hence, we constructed variants of thioredoxin-mouse NT-proCNP(1–50) where SRLLR residues (i.e. those immediately downstream from the LKGDR201 site in NT-proCNP(1–50)) were systematically added one at a time downstream of the internal DDDDK156 site. To evaluate the relative effects of site accessibility and downstream sequence context on the efficiency of enterokinase cleavage, we have also replaced the native LKGDR201 sequence with DDDDK201. Our results showed that incremental addition of SRLLR residues led to a steady increase in the rate of hydrolysis at DDDDK156. Further variants comprising DDDDK156SS, DDDDK156SD and DDDDK156RR showed that the minimal critical determinants for enhanced enterokinase cleavage are serine in the P1′ position followed by a serine or a basic residue, lysine or arginine, in the P2′ position. Our data provided conclusive evidence that the influence of downstream sequences on recombinant light chain enterokinase activity was greater than accessibility of the target site at the terminus region of the protein. We further showed that the catalytic efficiency of the native holoenzyme was influenced primarily by residues on the N-terminal side of the scissile bond while being neutral to residues on the C-terminal side. Finally, we found that cleavage of all nine fusion proteins reflects accurate hydrolysis at the DDDDK156 and DDDDK201 sites when recombinant light chain enterokinase was used while non-specific processing at secondary sites were observed when these fusion proteins were treated with the native holoenzyme.