Identification of potential active-site residues in the Escherichia coli leader peptidase

Catalytic hydroxyl/amine dyads within serine proteases

The 'catalytic triad' mechanism, which involves a serine, histidine and aspartic acid, has become synonymous with serine proteases. However, recently, mechanistically novel serine proteases have been discovered. These proteases use hydroxyl/epsilon-amine or hydroxyl/alpha-amine 'catalytic dyads' as their reactive centers.

Molecular cloning and expression of the spsB gene encoding an essential type I signal peptidase from Staphylococcus aureus

The gene, spsB, encoding a type I signal peptidase has been cloned from the gram-positive eubacterium Staphylococcus aureus. The gene encodes a protein of 191 amino acid residues with a calculated molecular mass of 21,692 Da. Comparison of the protein sequence with those of known type I signal peptidases indicates conservation of amino acid residues known to be important or essential for catalytic activity. The enzyme has been expressed to high levels in Escherichia coli and has been demonstrated to possess enzymatic activity against E. coli preproteins in vivo. Experiments whereby the spsB gene was transferred to a plasmid that is temperature sensitive for replication indicate that spsB is an essential gene. We identified an open reading frame immediately upstream of the spsB gene which encodes a type I signal peptidase homolog of 174 amino acid residues with a calculated molecular mass of 20,146 Da that is predicted to be devoid of catalytic activity.

Identification of Trp300 as an important residue for Escherichia coli leader peptidase activity

We previously reported that leader peptidase from Escherichia coli was extensively inactivated by reaction with N-bromosuccinimide with concomitant and selective modification of the Trp300 and Trp310 residues [Kim, Y.-T., Muramatsu, T. & Takahashi, K. (1995) J. Biochem. (Tokyo) 117, 535-544]. This indicated that one or both of these tryptophan residues are important for the activity of the enzyme. In order to define further the role of individual tryptophan residues in the activity of leader peptidase, site-directed mutagenesis studies were performed to replace each tryptophan residue with phenylalanine and/or alanine. The replacements of Trp20, Trp59, Trp261, Trp284, and Trp310 with phenylalanine hardly affected the enzyme activity toward a synthetic peptide substrate and the ability to complement the temperature sensitivity of the mutant leader peptidase in E. coli IT41. In contrast, the activity toward the synthetic substrate was significantly decreased by replacement of Trp300 with phenylalanine or alanine. The kcat values of the W300F and W300A mutant enzymes were reduced to 42% and 22%, respectively, of that of the wild-type enzyme, whereas the Km values of these mutant enzymes were almost identical with that of the wild-type enzyme. Moreover, the complementing ability in E. coli IT41 was lost (almost) completely when Trp300 was replaced with phenylalanine or alanine. These results strongly indicate that Trp300 in leader peptidase is important for the catalytic mechanism and/or the construction of the active site structure of the enzyme.

Crystallization of a soluble, catalytically active form of Escherichia coli leader peptidase

Leader peptidase, a novel serine protease in Escherichia coli, catalyzes the cleavage of the amino-terminal leader sequences from exported proteins. It is an integral membrane protein containing two transmembrane segments with its carboxy-terminal catalytic domain residing in the periplasmic space. Here, we report a procedure for the purification and the crystallization of a soluble non-membrane-bound form of leader peptidase (delta 2-75). Crystals were obtained by the sitting-drop vapor diffusion technique using ammonium dihydrogen phosphate as the precipitant. Interestingly, we have found that the presence of the detergent Triton X-100 is required to obtain crystals sufficiently large for X-ray analysis. The crystals belong to the tetragonal space group P4(2)2(1)2, with unit cell dimensions of a = b = 115 A and c = 100 A, and contain 2 molecules per asymmetric unit. This is the first report of the crystallization of a leader (or signal) peptidase.

Signal sequence processing in rough microsomes

Secretory proteins are synthesized with a signal sequence that is usually cleaved from the nascent protein during the translocation of the polypeptide chain into the lumen of the endoplasmic reticulum. To determine the fate of a cleaved signal sequence, we used a synchronized in vitro translocation system. We found that the cleaved signal peptide of preprolactin is further processed close to its COOH terminus. The resulting fragment accumulated in the microsomal fraction and with time was released into the cytosol. Signal sequence cleavage and processing could be reproduced with reconstituted vesicles containing Sec61, signal recognition particle receptor, and signal peptidase complex.

Characterization of a soluble, catalytically active form of Escherichia coli leader peptidase: requirement of detergent or phospholipid for optimal activity

Leader peptidase is a novel serine protease in Escherichia coli, which functions to cleave leader sequences from exported proteins. Its catalytic domain extends into the periplasmic space and is anchored to the membrane by two transmembrane segments located at the N-terminal end of the protein. At present, there is no information on the structure of the catalytic domain. Here, we report on the properties of a soluble form of leader peptidase (delta 2-75), and we compare its properties to those of the wild-type enzyme. We find that the truncated leader peptidase has a kcat of 3.0 S-1 and a Km of 32 microM with a pro-OmpA nuclease A substrate. In contrast to the wild-type enzyme (pI of 6.8), delta 2-75 is water-soluble and has an acidic isoelectric point of 5.6. We also show with delta 2-75 that the replacement of serine 90 and lysine 145 with alanine residues results in a 500-fold reduction in activity, providing further evidence that leader peptidase employs a catalytic serine/lysine dyad. Finally, we find that the catalysis of delta 2-75 is accelerated by the presence of the detergent Triton X-100, regardless if the substrate is pro-OmpA nuclease A or a peptide substrate. Triton X-100 is required for optimal activity of delta 2-75 at a level far below the critical micelle concentration. Moreover, we find that E. coli phospholipids stimulate the activity of delta 2-75, suggesting that phospholipids may play an important physiological role in the catalytic mechanism of leader peptidase.

Identification of the potential active site of the signal peptidase SipS of Bacillus subtilis. Structural and functional similarities with LexA-like proteases

Signal peptidases remove signal peptides from secretory proteins. By comparing the type I signal peptidase, SipS, of Bacillus subtilis with signal peptidases from prokaryotes, mitochondria, and the endoplasmic reticular membrane, patterns of conserved amino acids were discovered. The conserved residues of SipS were altered by site-directed mutagenesis. Replacement of methionine 44 by alanine yielded an enzyme with increased activity. Two residues (aspartic acid 146 and arginine 84) appeared to be conformational determinants; three other residues (serine 43, lysine 83, and aspartic acid 153) were critical for activity. Comparison of SipS with other proteases requiring serine, lysine, or aspartic acid residues in catalysis revealed sequence similarity between the region of SipS around serine 43 and lysine 83 and the active-site region of LexA-like proteases. Furthermore, self-cleavage sites of LexA-like proteases closely resembled signal peptidase cleavage sites. Together with the finding that serine and lysine residues are critical for activity of the signal peptidase of Escherichia coli (Tschantz, W.R., Sung, M., Delgado-Partin, V.M., and Dalbey, R.E. (1993) J. Biol. Chem. 268, 27349-27354), our data indicate that type I signal peptidases and LexA-like proteases are structurally and functionally related serine proteases. A model envisaging a catalytic serine-lysine dyad in prokaryotic type I signal peptidases is proposed to accommodate our observations.

Cloning and sequence analysis of a signal peptidase I from the thermophilic cyanobacterium Phormidium laminosum

Type I signal peptidases are a widespread family of enzymes which remove the presequences from proteins translocated across cell membranes, including thylakoid and cytoplasmic membranes of cyanobacteria and thylakoid membranes of chloroplasts. We have cloned and sequenced a signal peptidase gene from the thermophilic cyanobacterium Phormidium laminosum which is believed to encode an enzyme common to both membrane systems. The deduced amino acid sequence is 203 residues long and although the overall similarity among signal peptidases is rather low there are a number of identifiable conserved regions present. The P. laminosum enzyme is predicted to have a single transmembrane domain, in contrast to other Gram-negative bacterial sequences, but similar to other type I signal peptidases.

The DsbA-DsbB system affects the formation of disulfide bonds in periplasmic but not in intramembraneous protein domains

The DsbA and DsbB proteins of Escherichia coli are involved in facilitating the formation of disulfide bonds in periplasmic proteins. Here, we show that the rate of formation of a disulfide bond in the periplasmic domain of the inner membrane protein leader peptidase is reduced in dsbA and dsbB strains, whereas the rate of formation of a disulfide bond engineered into the membrane embedded domain of the same protein is completely unaffected by these mutations. We conclude that the Dsb proteins do not facilitate the formation of intramembraneous disulfides.

Evidence that the catalytic activity of prokaryote leader peptidase depends upon the operation of a serine-lysine catalytic dyad

Leader peptidase (LP) is the enzyme responsible for proteolytic cleavage of the amino acid leader sequence from bacterial preproteins. Recent data indicate that LP may be an unusual serine proteinase which operates without involvement of a histidine residue (M. T. Black, J. G. R. Munn, and A. E. Allsop, Biochem. J. 282:539-543, 1992; M. Sung and R. E. Dalbey, J. Biol. Chem. 267:13154-13159, 1992) and that, therefore, one or more alternative residues must perform the function of a catalytic base. With the aid of sequence alignments, site-specific mutagenesis of the gene encoding LP (lepB) from Escherichia coli has been employed to investigate the mechanism of action of the enzyme. Various mutant forms of plasmid-borne LP were tested for their abilities to complement the temperature-sensitive activity of LP in E. coli IT41. Data are presented which indicate that the only conserved amino acid residue possessing a side chain with the potential to ionize, and therefore with the potential to transfer protons, which cannot be substituted with a neutral side chain is lysine at position 145. The data suggest that the catalytic activity of LP is dependent on the operation of a serine-lysine catalytic dyad.

Signal peptidases in prokaryotes and eukaryotes--a new protease family

Signal peptidases remove targeting peptides from pre-proteins and play central roles in the secretory pathway, as well as in the delivery of proteins to the mitochondrial intermembrane space and to the lumen of thylakoids. The catalytic mechanism of pre-protein cleavage has long been an enigma, but recent data from site-directed mutagenesis and sequence alignment studies suggest that signal peptidases may constitute a new type of serine protease, mechanistically related to the beta-lactamases.