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.
Learning from Nature's Drug Factories: Nonribosomal Synthesis of Macrocyclic Peptides
Stephan A. Sieber and Mohamed A. Marahiel*
Fachbereich
Chemie/Biochemie, Philipps-Universität Marburg, 35032 Marburg,
Germany
 |
INTRODUCTION
|
|---|
With the discovery of penicillin as an efficient antibacterial agent
isolated from the fungus Penicillium notatum,
microorganisms attracted considerable attention as a new source for
pharmaceutical agents. Screening of microbial extracts revealed the
large structural diversity of natural compounds with broad biological
activities, such as antimicrobial, antiviral, immunosuppressive, and
antitumor activities. Like penicillin, many of these products are small
peptide molecules consisting of 3 to 22 residues with often unusual
structural elements. These include heterocyclic elements,D-amino acids, and glycosylated and N-methylated residues,
suggesting a nonribosomal origin of biosynthesis. Due to the potent
pharmacological activities of these compounds, there was an
overwhelming interest in exploring their mechanism of synthesis.
Lipmann et al. reported as early as the 1970s that the cyclic peptides
gramicidin S and tyrocidine from Bacillus spp. were produced
in a nucleic acid-independent way through the use of large enzyme
complexes similar to fatty acid synthases
(17). Subsequently, other
peptidic natural products were shown to be assembled by large enzymes,
referred to as nonribosomal peptide synthetases (NRPS), which utilize
the multiple-carrier thiotemplate mechanism
(34). A common feature of
many nonribosomally produced peptides is their constrained structure,
which ensures a precise functionality important for a proper
interaction with the dedicated molecular target in the cell. Nature
achieves this rigidity in molecular structure through several
strategies: the molecule can be oxidatively cross-linked, as in
vancomycin, heterocyclized, as in penicillin or, more commonly,
cyclized, as in fengycin (Fig.
1). Cyclization seems to be the predominant way of constraining
nonribosomally synthesized peptides. Because peptide cyclization from
the point of view of chemical synthesis is difficult to achieve without
protection of all of the side chains, there has been rapidly growing
interest in exploration of the enzymatic cyclization mechanism for the
development of new synthesis routes.
 |
A SHORT WALK DOWN THE
NRPS ASSEMBLY LINE
|
|---|
The nonribosomal machinery for peptide
synthesis uses large multienzyme complexes as an assembly line to
catalyze stepwise peptide condensation. The substrates of these
multienzyme complexes are not restricted to the 20 amino
acids, since hundreds of building blocks are now known to be integrated
and modified by postsynthesis action. Common to this assembly line is
the incorporation of nonproteinogenic amino acids, such as
D-isomers, carboxy acids, and N-methylated residues, as well
as the incorporation of heterocyclic rings and fatty acids (Fig.
1). Glycosylation and
oxidative cross-linking are common further postsynthetic modifications
by enzymes that are associated with the NRPS machinery.
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.

View larger version (35K):
[in this window]
[in a new window]
|
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.
|
|
Beside the A,
T, and C domains, which are essential domains of an elongation module,
there are also other, optional domains. A common structural motif of
nonribosomal peptides is the incorporation of D-amino acids,
which is mediated by the epimerization domain (E domain; about 450
amino acids). The E domain catalyzes the racemization of the
T-domain-bound amino acid to form an equilibrium between the
L and D conformers. However, the C domain
incorporates only the D-amino acid into the growing peptide
chain (16). In the
surfactin synthetase, two epimerization domains in modules 3 and 6 are
responsible for the racemization of T-domain-bound L-Leu.
The combination of L- and D-amino acids gives the
peptide a unique conformation that is important for the specific
interaction with its cellular target.
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.
 |
CYCLIZATION STRATEGIES: NATURE'S
WAY
|
|---|
All known NRPS macrocyclization strategies lead to cyclic or
cyclic branched-chain peptides (Fig.
1). In macrolactones, the
branch point can be either a hydroxylated amino acid side chain or a
hydroxylated fatty acid moiety. For the surfactin peptide cyclase, the
ring closure is enzymatically catalyzed between an N-terminal
ß-hydroxyl fatty acid and the C-terminal peptide end
(32). Cyclization was
observed only when the (R)-ß-hydroxyl fatty acid was
used, while the (S)-enantiomer showed only enzymatic
hydrolysis, indicating stereoselective recognition
(12). The
lipodepsipeptide cyclic product is a strong detergent with antiviral,
hemolytic, and antibacterial activities
(21). A major
contribution to the detergent activity is provided by the lipopeptide
chain, which is believed to be transferred to the
N-terminal residue during the initiation reaction by a fatty acid
acyltransferase. In contrast, the syringomycin (Pseudomonas
syringae) and fengycin (B. subtilis)
lipopeptide cyclases accept serine and tyrosine side chains of the
peptide sequence as nucleophiles for cyclization, discriminating the
N-terminal ß-hydroxyl group of the attached fatty acid moiety
(24,
26,
33) (Fig.
1). Moreover, these
peptide cyclases display a very high level of regioselectivity by
selecting only one specific residue of the substrate from a large
source of nucleophiles for cyclization.
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.
 |
CHEMOENZYMATIC CYCLIZATION
|
|---|
The great
pharmacological potential of many cyclic peptides emphasizes their role
in drug discovery, as they show specific interactions with cellular
targets and a high level of resistance to proteolytic enzymes. They are
therefore most promising scaffolds for pharmacophores. So far,
synthetic chemistry faces several difficulties in the production of
cyclic compounds providing sufficiently good yields and
regioselectivity. Although cyclization is an entropically favorable
process, synthetic macrocyclization is difficult to achieve, since
steric repulsion of ring residues as well as the use of protecting
groups to ensure proper regiochemistry decreases yields and makes
chemical synthetic operations expensive and rather difficult. Since
nature developed stereo- and regioselective peptide cyclization
enzymes, researchers have aimed to combine chemical linear peptide
synthesis with enzymatically catalyzed cyclization. This approach
allows easy synthesis of linear peptide sequences by established
solid-phase peptide chemistry, followed by selective and efficient
enzymatic cyclization without the use of protecting groups and the
formation of undesirable by-products.
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).

View larger version (26K):
[in this window]
[in a new window]
|
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.
|
|
In addition
to their use with the tyrocidine peptide cyclase, SNAC substrates also
were used to characterize the cyclization of gramicidin S and surfactin
(12,
32). In contrast to the
tyrocidine peptide cyclase, the surfactin peptide cyclase showed much
less substrate tolerance, indicating differences in the binding pockets
of these enzymes. While the tyrocidine peptide cyclase was capable of
cyclizing shorter and longer SNAC substrates, the surfactin peptide
cyclase showed only SNAC hydrolysis for shorter and longer compounds.
Moreover, a change in the N-terminal nucleophilic attacking group from
an amine to a hydroxyl group in the tyrocidine sequence resulted in no
change in the cyclization outcome, while an opposite change from a
hydroxyl fatty acid to an amino fatty acid group in the surfactin
sequence resulted in only hydrolysis and not cyclization. An important
feature of cyclic peptides is the ß-sheet content, which is
high for molecules with (4n + 2) residues
(12,
31). A peptide with a
high ß-sheet content, such as the dekapeptide tyrocidine
(n = 2), facilitates cyclization through substrate
preorganization by backbone-to-backbone hydrogen bonds. This intrinsic
property of tyrocidine facilitates easy cyclization, which was also
reported to occur without catalysis, but at a lower efficiency
(3). In contrast, the
heptapeptide surfactin displays fewer ß sheets and therefore no
substantial substrate preorganization. The ß-sheet contents in
the peptide sequences of surfactin and tyrocidine therefore also may
contribute to the observed differences in substrate tolerance.
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.
 |
STRUCTURAL AND MECHANISTIC
ASPECTS OF NRPS PEPTIDE CYCLASES
|
|---|
The three-dimensional
organization of enzyme residues encodes all information required to
understand the principles and general features of macrocyclization.
Regiospecific selection of only one nucleophile for cyclization and the
exclusion of water to prevent undesired hydrolysis are features which
are embedded in the structural fold. Moreover, the question of how
thioesterases from different NRPS systems catalyze termination in one
case by cyclization and in another case by hydrolysis needs to be
elucidated. Crystallographic data for the excised surfactin peptide
cyclase (TE domain) showed that this enzyme is a member of the
,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.

View larger version (64K):
[in this window]
[in a new window]
|
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.
|
|
Further studies of enzymatic substrate recognition
elements for the surfactin peptide cyclase were carried out by using a
detailed substrate scan and cocrystallization analysis for enzyme-bound
inhibitor-substrate. The crystallization studies revealed
well-defined binding pockets for the two C-terminal leucine residues in
the enzyme, while the rest of the peptide sequence seems to be less
well coordinated (32)
(Fig. 4C). In the
deacylation step of the reaction, the ß-hydroxyl group of the
fatty acid moiety is activated by the same histidine and aspartate to
facilitate an intramolecular nucleophilic attack on the acyl-enzyme
ester bond to release the final lactone product. Many thioesterase
domains from other NRPS systems, e.g., vancomycin, as well as
structurally related lipases only hydrolyze and do not cyclize their
products. A sequence alignment between the surfactin peptide cyclase
and other members of the
,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.
 |
CONCLUDING REMARKS
|
|---|
Research efforts
of the past few years in the growing field of enzymatic peptide
cyclization in nonribosomal peptide synthesis, summarized in this
article, have revealed substantial insights into the architectural,
mechanistic, and functional organization of NRPS peptide cyclases.
Based on the diversity of natural cyclization strategies,
chemoenzymatic approaches were developed to allow cross talk between
biology and chemistry to reprogram natural peptide sequences by
chemical peptide synthesis and subsequent enzymatic cyclization. This
method can serve as a new source of small cyclic peptide molecules with
altered or improved pharmacological activities. Since these enzyme
catalysts are valuable tools for the synthesis of cyclic molecules,
future research efforts also will concentrate on in vitro protein
evolution to generate custom-made catalysts for cyclization of a given
peptide sequence.
 |
ACKNOWLEDGMENTS
|
|---|
This work was supported by
Studienstiftung des Deutschen Volkes (SAS) and Deutsche
Forschungsgemeinschaft
(MAM).
 |
FOOTNOTES
|
|---|
* Corresponding
author. Mailing address: Fachbereich Chemie/Biochemie,
Philipps-Universität Marburg, Hans-Meerwein-Str., 35032 Marburg,
Germany. Phone: 49 6421 2825722. Fax: 49 6421 2822191. E-mail:
marahiel{at}chemie.uni-marburg.de. 
 |
REFERENCES
|
|---|
- Belshaw,
P. J., C. T. Walsh, and T. Stachelhaus.1999
. Aminoacyl-CoAs as probes of condensation domain
selectivity in nonribosomal peptide synthesis. Science
284:486-489.[Abstract/Free Full Text]
- Bruner,
S. D., T. Weber, R. M. Kohli, D. Schwarzer,
M. A. Marahiel, C. T. Walsh, and M. T.
Stubbs. 2002. Structural basis for the cyclization of
the lipopeptide antibiotic surfactin by the thioesterase domain SrfTE.Structure (Cambridge)
10:301-310.
- Bu,
X., X. Wu, G. Xie, and Z. Guo. 2002. Synthesis of
tyrocidine A and its analogues by spontaneous cyclization in aqueous
solution. Org. Lett.
4:2893-2895.[CrossRef][Medline]
- Conti,
E., T. Stachelhaus, M. A. Marahiel, and P. Brick.1997
. Structural basis for the activation of
phenylalanine in the non-ribosomal biosynthesis of gramicidin S. EMBO
J.
16:4174-4183.[CrossRef][Medline]
- Craik,
D. J., N. L. Daly, I. Saska, M. Trabi, and
K. J. Rosengren. 2003. Structures of
naturally occurring circular proteins from bacteria. J.
Bacteriol.
185:4011-4021.[Free Full Text]
- de
Crecy-Lagard, V., W. Saurin, D. Thibaut, P. Gil, L. Naudin, J. Crouzet,
and V. Blanc. 1997. Streptogramin B biosynthesis in
Streptomyces pristinaespiralis and
Streptomyces virginiae: molecular characterization of
the last structural peptide synthetase gene. Antimicrob. Agents
Chemother.
41:1904-1909.[Abstract]
- Dieckmann,
R., Y. O. Lee, H. van Liempt, H. von Dohren, and H.
Kleinkauf. 1995. Expression of an active
adenylate-forming domain of peptide synthetases corresponding to
acyl-CoA-synthetases. FEBS Lett.
357:212-216.[CrossRef][Medline]
- Duitman,
E. H., L. W. Hamoen, M. Rembold, G. Venema, H.
Seitz, W. Saenger, F. Bernhard, R. Reinhardt, M. Schmidt, C. Ullrich,
T. Stein, F. Leenders, and J. Vater. 1999. The
mycosubtilin synthetase of Bacillus subtilis
ATCC6633: a multifunctional hybrid between a peptide synthetase, an
amino transferase, and a fatty acid synthase. Proc. Natl. Acad.
Sci. USA
96:13294-13299.[Abstract/Free Full Text]
- Gehring,
A. M., I. Mori, and C. T. Walsh.1998
. Reconstitution and characterization of the
Escherichia coli enterobactin synthetase from EntB,
EntE, and EntF. Biochemistry
37:2648-2659.[CrossRef][Medline]
- Hubbard,
B. K., and C. T. Walsh. 2003.
Vancomycin assembly: nature's way. Angew. Chem. Int. Ed.
Engl.
42:730-765.[CrossRef][Medline]
- Keating,
T. A., C. G. Marshall, C. T. Walsh, and
A. E. Keating. 2002. The structure of VibH
represents nonribosomal peptide synthetase condensation, cyclization
and epimerization domains. Nat. Struct. Biol.
9:522-526.[Medline]
- Kohli,
R. M., J. W. Trauger, D. Schwarzer, M. A.
Marahiel, and C. T. Walsh. 2001. Generality
of peptide cyclization catalyzed by isolated thioesterase domains of
nonribosomal peptide synthetases. Biochemistry
40:7099-7108.[Medline]
- Kohli,
R. M., C. T. Walsh, and M. D.
Burkart. 2002. Biomimetic synthesis and optimization
of cyclic peptide antibiotics. Nature
418:658-661.[CrossRef][Medline]
- Konz,
D., A. Klens, K. Schorgendorfer, and M. A. Marahiel.1997
. The bacitracin biosynthesis operon of
Bacillus licheniformis ATCC 10716: molecular
characterization of three multi-modular peptide synthetases.Chem. Biol.
4:927-937.[CrossRef][Medline]
- Lambalot,
R. H., A. M. Gehring, R. S. Flugel, P.
Zuber, M. LaCelle, M. A. Marahiel, R. Reid, C. Khosla, and
C. T. Walsh. 1996. A new enzyme
superfamilythe phosphopantetheinyl transferases. Chem.
Biol.
3:923-936.[CrossRef][Medline]
- Linne,
U., and M. A. Marahiel. 2000. Control of
directionality in nonribosomal peptide synthesis: role of the
condensation domain in preventing misinitiation and timing of
epimerization. Biochemistry
39:10439-10447.[CrossRef][Medline]
- Lipmann,
F., W. Gevers, H. Kleinkauf, and R. Roskoski, Jr.1971
. Polypeptide synthesis on protein templates: the
enzymatic synthesis of gramicidin S and tyrocidine. Adv.
Enzymol. Relat. Areas Mol. Biol.
35:1-34.[CrossRef][Medline]
- Marahiel,
M. A., T. Stachelhaus, and H. D. Mootz.1997
. Modular peptide synthetases involved in
non-ribosomal peptide synthesis. Chem. Rev.
97:2651-2673.[CrossRef][Medline]
- May,
J. J., T. M. Wendrich, and M. A.
Marahiel. 2001. The dhb operon of Bacillus
subtilis encodes the biosynthetic template for the catecholic
siderophore 2,3-dihydroxybenzoate-glycine-threonine trimeric ester
bacillibactin. J. Biol. Chem.
276:7209-7217.[Abstract/Free Full Text]
- Mootz,
H. D., D. Schwarzer, and M. A. Marahiel.2002
. Ways of assembling complex natural products on
modular nonribosomal peptide synthetases. Chembiochem
3:490-504.[CrossRef][Medline]
- Peypoux,
F., J. M. Bonmatin, and J. Wallach. 1999.
Recent trends in the biochemistry of surfactin. Appl. Microbiol.
Biotechnol.
51:553-563.[CrossRef][Medline]
- Reuter,
K., M. R. Mofid, M. A. Marahiel, and R. Ficner.1999
. Crystal structure of the surfactin
synthetase-activating enzyme Sfp: a prototype of the
4'-phosphopantetheinyl transferase superfamily. EMBO
J.
18:6823-6831.[CrossRef][Medline]
- Scholz-Schroeder,
B. K., J. D. Soule, and D. C. Gross.2003
. The sypA, sypS, and sypC synthetase genes encode
twenty-two modules involved in the nonribosomal peptide synthesis of
syringopeptin by Pseudomonas syringae pv.
syringae B301D. Mol. Plant-Microbe Interact.
16:271-280.[Medline]
- Scholz-Schroeder,
B. K., J. D. Soule, S. E. Lu, I.
Grgurina, and D. C. Gross. 2001. A physical
map of the syringomycin and syringopeptin gene clusters localized to an
approximately 145-kb DNA region of Pseudomonas
syringae pv. syringae strain B301D.Mol. Plant-Microbe Interact.
14:1426-1435.[Medline]
- Schwarzer,
D., R. Finking, and M. A. Marahiel. 2003.
Nonribosomal peptides: from genes to products. Nat. Prod.
Rep.
20:275-287.[CrossRef][Medline]
- Segre,
A., R. C. Bachmann, A. Ballio, F. Bossa, I. Grgurina,
N. S. Iacobellis, G. Marino, P. Pucci, M. Simmaco, and
J. Y. Takemoto. 1989. The structure
of syringomycins A1, E and G. FEBS Lett.
255:27-31.[CrossRef][Medline]
- Shaw-Reid,
C. A., N. L. Kelleher, H. C. Losey,
A. M. Gehring, C. Berg, and C. T. Walsh.1999
. Assembly line enzymology by multimodular
nonribosomal peptide synthetases: the thioesterase domain of E. coli
EntF catalyzes both elongation and cyclolactonization. Chem.
Biol.
6:385-400.[CrossRef][Medline]
- Sieber,
S. A., C. T. Walsh, and M. A.
Marahiel. 2003. Loading peptidyl-coenzyme A onto
peptidyl carrier proteins: a novel approach in characterizing
macrocyclization by thioesterase domains. J. Am. Chem.
Soc.
125:10862-10866.[CrossRef][Medline]
- Stachelhaus,
T., A. Hüser, and M. A. Marahiel.1996
. Biochemical characterization of peptidyl carrier
protein (PCP), the thiolation domain of multifunctional peptide
synthetases. Chem. Biol.
3:913-921.[CrossRef][Medline]
- Trauger,
J., R. Kohli, H. Mootz, M. Marahiel, and C. Walsh.2000
. Peptide cyclization catalysed by the thioesterase
domain of tyrocidine synthetase. Nature
407:215-218.[CrossRef][Medline]
- Trauger,
J. W., R. M. Kohli, and C. T. Walsh.2001
. Cyclization of backbone-substituted peptides
catalyzed by the thioesterase domain from the tyrocidine nonribosomal
peptide synthetase. Biochemistry
40:7092-7098.[Medline]
- Tseng,
C. C., S. D. Bruner, R. M. Kohli,
M. A. Marahiel, C. T. Walsh, and S. A.
Sieber. 2002. Characterization of the surfactin
synthetase C-terminal thioesterase domain as a cyclic depsipeptide
synthase. Biochemistry
41:13350-13359.[CrossRef][Medline]
- Vanittanakom,
N., W. Loeffler, U. Koch, and G. Jung. 1986.
Fengycina novel antifungal lipopeptide antibiotic produced by
Bacillus subtilis F-29-3. J. Antibiot.
(Tokyo)
39:888-901.[Medline]
- Walsh,
C. T. 2003. Antibiotics: actions, origins,
and resistance, p. 195-220. ASM Press, Washington,
D.C.
- Weber, G.,
and E. Leitner. 1994. Disruption of the cyclosporin
synthetase gene of Tolypocladium niveum. Curr.
Genet.
26:461-467.[CrossRef][Medline]
- Weber,
T., R. Baumgartner, C. Renner, M. A. Marahiel, and
T. A. Holak. 2000. Solution structure of
PCP, a prototype for the peptidyl carrier domains of modular peptide
synthetases. Struct. Fold Des.
8:407-418.[Medline]
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.
This article has been cited by other articles:
-
Duitman, E. H., Wyczawski, D., Boven, L. G., Venema, G., Kuipers, O. P., Hamoen, L. W.
(2007). Novel Methods for Genetic Transformation of Natural Bacillus subtilis Isolates Used To Study the Regulation of the Mycosubtilin and Surfactin Synthetases. Appl. Environ. Microbiol.
73: 3490-3496
[Abstract]
[Full Text]
-
Wu, C.-Y., Chen, C.-L., Lee, Y.-H., Cheng, Y.-C., Wu, Y.-C., Shu, H.-Y., Gotz, F., Liu, S.-T.
(2007). Nonribosomal Synthesis of Fengycin on an Enzyme Complex Formed by Fengycin Synthetases. J. Biol. Chem.
282: 5608-5616
[Abstract]
[Full Text]
-
Grunewald, J., Marahiel, M. A.
(2006). Chemoenzymatic and Template-Directed Synthesis of Bioactive Macrocyclic Peptides. Microbiol. Mol. Biol. Rev.
70: 121-146
[Abstract]
[Full Text]
-
Puk, O., Bischoff, D., Kittel, C., Pelzer, S., Weist, S., Stegmann, E., Sussmuth, R. D., Wohlleben, W.
(2004). Biosynthesis of Chloro-{beta}-Hydroxytyrosine, a Nonproteinogenic Amino Acid of the Peptidic Backbone of Glycopeptide Antibiotics. J. Bacteriol.
186: 6093-6100
[Abstract]
[Full Text]
-
Walsh, C. T.
(2004). Polyketide and Nonribosomal Peptide Antibiotics: Modularity and Versatility. Science
303: 1805-1810
[Abstract]
[Full Text]