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Journal of Bacteriology, December 2003, p. 7036-7043, Vol. 185, No. 24
0021-9193/03/$08.00+0 DOI: 10.1128/JB.185.24.7036-7043.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
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Fachbereich Chemie/Biochemie, Philipps-Universität Marburg, 35032 Marburg, Germany
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FIG. 1. Naturally
occurring macrolactones and
macrolactams.
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In order
to understand the principles of this enzymatically directed peptide
synthesis, the mechanistic features of NRPS are briefly summarized with
the surfactin synthetase from Bacillus subtilis as an
example (see also references
18,
20,
25, and
34). The surfactin
synthetase is a large multienzyme complex consisting of three enzymatic
subunits, SrfA (402 kDa), SrfB (401 kDa), and SrfC (144 kDa), which
consist of seven modules that comprise 24 catalytic domains (Fig.
2). Each module is responsible for the specific incorporation of one
dedicated substrate into the growing heptapeptide chain
(21). The N-terminal
module of an assembly line, the initiation module, specifically
recognizes and activates the N-terminal amino acid of the peptide
product. All chemical reactions necessary to incorporate and modify
each substrate are mediated by a catalytically independent set of
domains incorporated within the modules. The first step in biosynthesis
is the recognition and activation of a dedicated substrate by the
adenylation domain (A domain; about 550 amino acids)
(4). By analogy to
aminoacyl-tRNA synthetase, the A domain catalyzes the activation of a
substrate as aminoacyladenylate through the
Mg2+-dependent hydrolysis of ATP and the release of
pyrophoshate (7). In the
next step, the aminoacyladenylate intermediate is transferred to the
free thio group of the cofactor phosphopantetheine, which is tethered
to the thiolation domain (T domain, or peptidyl carrier protein; about
80 amino acids) located downstream of the A domain
(29,
36). The
phosphopantetheine arm is attached to an invariant serine residue of
the apo-T domain by a dedicated 4'-phosphopantetheine (ppan)
transferase that uses coenzyme A (CoA) as a substrate
(15,
22). The intermediates,
tethered by the reactive thioester to the flexible cofactor
phosphopantetheine (in each module), can be transferred to other
domains for subsequent catalytic reactions. Peptide bond formation
between two adjacent substrates is catalyzed by the condensation domain
(C domain; about 450 amino acids), which is located between the A and T
domains of subsequent modules
(11). The C domain
catalyzes the nucleophilic attack of the amino acid bound to the
downstream T domain with its free
-amino group on the
activated thioester of the upstream T-domain-bound intermediate
(1). For the surfactin
initiation reaction, peptide bond formation occurs between modules 1
and 2 by the nucleophilic attack of the
-amino group of
leucine on the thioester-activated carboxy group of glutamate to give a
dipeptide which is then translocated to module 2.
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FIG. 2. NRPS
assembly of surfactin. The surfactin synthetase consists of 24
individual domains responsible for the catalysis of 24 chemical
reactions. These domains catalyze activation (A domain), covalent
binding (T domain), elongation (C domain), epimerization (E domain),
and release (TE domain) by either cyclization or hydrolysis. The
domains are organized in modules (indicated in blue and red), where
each module incorporates one dedicated building block into the growing
peptide chain. The peptide chain is covalently tethered to the
multienzyme via the cofactor phosphopantetheine (ppan), and synthesis
proceeds according to the enzymatic template from the N- to the
C-terminal end. FA, fatty acid
chain.
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All catalytic domains discussed so far are repeating units of the enzymatic template and contribute to the synthesis of a linear peptide molecule tethered to the multienzyme. In order to reactivate the multienzyme for a next synthesis cycle, the mature peptide must be cleaved once it reaches the end of the assembly line. This reaction usually is accomplished by a thioesterase domain (TE domain; about 280 amino acids) fused to the C-terminal module. The peptide can be released either by hydrolysis as a linear acid or by an intramolecular reaction with an internal nucleophile to give a cyclic peptide. Hydrolytic release is observed, e.g., for vancomycin, whose peptide backbone is constrained by further postsynthetic oxidative cross-linking reactions (10). For surfactin, the peptide backbone is constrained by the intramolecular nucleophilic attack of a ß-hydroxyl group of the fatty acid moiety to give a branched-chain lipodepsipeptide (32) (Fig. 1). Many other cyclization strategies give rise to a large and diverse set of cyclic or cyclic branched molecules with distinct biological activities. A TE domain catalyzing a cyclization reaction also is referred to as a peptide cyclase.
In addition to macrolactonization, natural product diversity also is increased by various enzymatic macrolactamization strategies. Basic head-to-tail peptide macrolactamization is observed in the antibiotic tyrocidine from Bacillus brevis and the potent immunosuppressive drug cyclosporin A from Tolypocladium niveum. In cyclosporin A, the final peptide bond is formed by a putative condensation domain (35) instead of a peptide cyclase, emphasizing that nature developed two enzyme species capable of catalyzing product release by cyclization. Besides head-to-tail cyclized lactams, branched-chain lactams also are observed. The peptide cyclase of the antifungal lipopetide mycosubtilin from B. subtilis forms regioselectively an amide bond between an N-terminal ß-amino fatty acid and the peptide C-terminal end (Fig. 1). As in surfactin, in mycosubtilin a fatty acid chain is involved in the cyclization process, providing an amine as a nucleophile (8). While the precursors in both cases seem to be ß-keto fatty acid residues derived from fatty acid synthases, nature processes these ketones in different ways. They are either reduced to a hydroxyl group, as observed in surfactin, or they are reductively aminated in a process catalyzed by aminotransferases, as observed in mycosubtilin. In both cases, nature uses a common precursor motif, which is subsequently diversified by the application of different synthetic strategies to increase the product outcome. As in fengycin and syringomycin, enzymatic amide bond formation also can occur between an ornithine side chain and the C-terminal peptide end, as observed in the antibiotic bacitracin from Bacillus licheniformis (14). The scope of cyclic lactames and lactones can be further broadened by oligomerization of peptide monomers. This additional strategy enables the B. brevis gramicidin S peptide cyclase to cyclodimerize two linear pentapeptides by catalyzing two subsequent peptide bond formation steps to form the cyclic lactam antibiotic gramicidin S (12) (Fig. 1). Also, cyclotrimerization is observed for the siderophore-forming peptide cyclases of enterobactin and the bacillibactin synthetase from Escherichia coli and B. subtilis, respectively (9, 19). Three units of 2,3-dihydroxybenzoyl-serine are fused together by three subsequent ester bond formation steps between the serine hydroxyl group of one molecule and the C-terminal end of another molecule to give the cyclic trilactone enterobactin. This lactone displays iron-chelating activity, which is closely related to its structure. Three intramolecular catechol ligands provide electron donors required for the coordination of iron, once more emphasizing the close relationship between cyclic structural organization and biological activity.
NRPS peptide cyclases can generate diverse cyclic peptide molecules ranging in size from very small, as in pristinamycin, with 7 residues, to very large, as in syringopeptin, with 22 residues (6, 23). At the large end of the scale is another source of macrocyclic molecules observed in nature, referred to as naturally occurring circular proteins (5). These proteins are of bacterial origin and have a folded three-dimensional structure. In contrast to NRPS, they are produced by the translation of genes. Cyclization occurs posttranslationally only in a head-to-tail fashion to produce a seamless circle of peptide bonds. In contrast to what is known for NRPS, not much is known about the cyclization mechanism of the linear precursors.
The cyclization strategies reported here emphasize that nature has developed a large enzymatic tool set which allows the introduction of diversity into linear peptide sequences by a variety of different cyclization steps. Selection from different nucleophiles, enantiomers, and positions in the peptide sequence makes peptide cyclases unique enzymatic tools with very specific intrinsic stereo- and regioselective recognition elements. Moreover, an understanding of the catalysis of one, two, or three subsequent condensation steps toward cyclization requires further studies of the structural and mechanistic aspects of these enzymes.
In order to achieve chemoenzymology, translation between the language of chemistry and the language of biology must be established by chemically mimicking the biological pathway as closely as possible. This was first achieved by Trauger et al., who cloned and overexpressed an excised peptide cyclase (28 kDa) from the tyrocidine synthetase (30). In order to prove the activity of this isolated enzyme versus that of the natural enzyme, which is embedded in a 724-kDa multienzyme complex, a short mimicked copy of the natural cofactor phosphopantetheine, N-acetylcysteamine (SNAC), was attached to the C-terminal end of a chemically synthesized linear tyrocidine peptide (Fig. 3A). SNAC represents a link between natural and artificial systems and is compatible with both. Incubation of the mimicked substrate and the excised peptide cyclase revealed activity with an observed cyclization/hydrolysis ratio of 6:1. The turnover of 59 min-1 indicated a very rapid conversion of the linear compound into the cyclic compound, indicating the usefulness of this enzyme as an in vitro biocatalyst (30). Follow-up studies with various peptidyl-SNAC substrates having various lengths, stereochemical properties, and amino acid compositions revealed that the tyrocidine peptide cyclase recognizes only C- and N-terminal residues of the substrate on the basis of identity and stereochemistry, leaving space for making longer and shorter substrates as well as for replacements of residues within the peptide backbone (12). A minimal recognition model was postulated (31). This observed substrate tolerance of the excised tyrocidine peptide cyclase allowed the synthesis of diverse tyrocidine variants in which position 4 (D-Phe) was replaced by 1 of 96 natural and unnatural amino acids. This library of tyrocidine product analogs was subsequently screened for improved or altered bioactivity. In contrast to the natural antibiotic tyrocidine, which does not discriminate between bacterial and eukaryotic cell membranes, the screen revealed that the substitution of D-Phe at position 4 with a positively charged D-amino acid led to a 30-fold increase in the selective recognition of bacterial membranes (13).
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FIG. 3. Chemoenzymatic
cyclization strategies. (A) Peptidyl-SNAC. The natural
cofactor phosphopantetheine T domain was mimicked for synthetic
substrates by attaching the last part of the cofactor, SNAC, to the
C-terminal end of the tyrocidine linear peptide chain. This soluble
substrate was subsequently incubated with the excised tyrocidine
cyclase (TE domain), and cyclic tyrocidine and a hydrolyzed product
were observed. (B) Peptidyl-CoA. Synthetically made fengycin
CoA is first loaded by the ppan transferase Sfp onto an invariant
serine residue of the apo-T domain from an excised fengycin T-TE
didomain. In the second step, the substrate is transferred to the
peptide cyclase (TE domain) by the nucleophilic attack of an invariant
serine residue of the TE domain active site on the peptidyl-ppan
thioester. Subsequent cyclization and hydrolysis are catalyzed by the
cyclase in the third step of the
reaction.
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To expand the set of cyclization catalysts, peptide cyclases from other NRPS systems, such as mycosubtilin and fengycin from B. subtilis and syringomycin from P. syringae, recently were cloned and overexpressed. Contrary to the observations for the surfactin and tyrocidine cyclases, no activity was observed for the mycosubtilin, fengycin, and syringomycin cyclases with synthetically made peptidyl-SNAC substrates, indicating a limitation in the chemoenzymatic potential of the latter cyclases. The inability to recognize or bind SNAC substrates in the active site of the excised peptide cyclase could be affected by the manner in which the short mimicked copy of SNAC is presented to the enzyme. To overcome this limitation, the cyclase domain (TE domain) was excised with the preceding cofactor-binding T domain as a T-TE didomain. Recombinant apo-T-TE cyclases then could be loaded in vitro with chemically synthesized peptidyl-CoA by using the ppan transferase Sfp. The resulting peptidyl-ppan-T-TE holocyclase carried the covalent cofactor-bound substrate in a way that mimicked the natural substrate presentation in the NRPS assembly line (28) (Fig. 3B). Incubation of fengycin T-TE cyclase with fengycin CoA and Sfp revealed cyclization and hydrolysis activities, which were not observed with SNAC substrates alone. These results indicate that the peptide needs to be directed into the peptide cyclase active site by the cofactor ppan to ensure correct enzyme recognition; in contrast, soluble substrates are not properly directed into the active site by diffusion. Cyclases which do not show activity with SNAC substrates seem to require covalent binding of the peptide substrate to the ppan T-domain in order to catalyze cyclic product formation.
,ß-hydrolase family
(2) (Fig.
4A). Since this was the first crystal structure determined for an NRPS
peptide cyclase, it served as a prototype for detailed mechanistic
investigations (32). The
structural similarity to serine hydrolases suggested that an
active-site catalytic triad is responsible for the macrocyclization
activity. This notion is in agreement with a recent structural model of
the surfactin cyclase which suggested that the ppan T-domain-bound
peptidyl chain is directed through a cleft into the active site of the
peptide cyclase and transferred to an invariant serine residue (Ser80),
which is activated by histidine (His207) and aspartate (Asp107)
(2) (Fig.
4B). The identity of this
catalytic triad was confirmed by mutational analysis, which showed that
all three residues were essential for enzyme activity
(32). The hydrophobic
surfactin peptidyl chain of the acyl-O-enzyme intermediate is
accommodated in a predominantly hydrophobic binding pocket with two
cationic residues predicted to direct cyclization through specific
interactions with the substrate (Fig.
4B). Mutation of these
residues to alanine resulted in a dramatic decrease in overall
activity, indicating their relevance for peptide
recognition.
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FIG. 4. Structural
data for surfactin cyclase SrfTE. (A) Surface (right) and
ribbon (left) representations of surfactin cyclase
( ,ß-hydrolase fold). The peptide substrate and the
ppan arm are modeled into a hydrophobic binding pocket and into a
substrate channel, respectively. Modeling with the T domain (yellow)
revealed a putative T-TE didomain docking site. (B)
Magnification of the binding pocket shows the catalytic triad (Ser80,
His207, and Asp107) and several hydrophobic residues, with the
exception of Lys111 and Arg120. (C) Cocrystallization study
of SrfTE with a boronic acid inhibitor substrate revealed specific
binding pockets for D-Leu6 and Leu7. Based on modeling
experiments, the rest of the peptide sequence seems to loop out of the
enzyme.
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,ß-hydrolase enzyme family
that catalyze only hydrolysis revealed the conservation among lipases
of a glycine residue involved in the formation of the oxyanion hole. In
the surfactin peptide cyclase, a proline residue is located at this
position. A mutation of proline to glycine resulted in a 12-fold change
in the product ratio in favor of hydrolysis, indicating that the change
from a rigid proline to a flexible glycine increases the conformational
freedom in this region of the active site and creates more access for
water to capture the acyl-enzyme intermediate
(32). This residue seems
to be a switch between hydrolysis and cyclization among
,ß-hydrolases. Detailed investigations of the surfactin peptide cyclase provided insights into mechanistic and architectural features of an enzyme which produces a branched cyclic lipodepsipeptide. Less is known about the mechanism and structure of other cyclases, particularly oligomerizing cyclases. A detailed mass spectrometric analysis was carried out for the last module of the enterobactin assembly line (EntF), containing a C-terminal peptide cyclase which catalyzes the cyclotrimerization of three 2,3-dihydroxybenzoyl-serine (DHB-Ser) units to give the cyclic trilactone enterobactin (27). In order to localize acyl-enzyme intermediates, an active-site histidine-to-alanine mutant enzyme with a very low substrate turnover was used. With this approach, it was possible to provide evidence for a covalent acyl-O-TE domain intermediate and demonstrate that the peptide cyclase is involved in two reactions: acyl-chain growth and cyclization. In the first steps of acyl-chain growth, DHB-Ser is transferred to the active-site serine of the peptide cyclase by the nucleophilic attack of active-site serine on the acyl-thioester of the upstream holo-T domain. The second step requires catalytic generation of a DHB-Ser alkoxide, which in turn allows nucleophilic attack on another DHB-Ser thioester-bound T domain to form a dimeric ester. The elongation step is repeated a third time before the final cyclic trilactone is released by the intramolecular nucleophilic attack of serine on the acyl-O-TE domain ester bond. This mechanistic analysis suggests that the enterobactin cyclase serves as a "waiting room" while the phosphopantetheinyl T domain is reacylated, a process which requires a stable ester bond and the exclusion of any water from the active site. Crystallographic data for this peptide cyclase and others will provide more insight into the overall mechanisms and allow for a comparison of their features.
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