The mechanism of MIO-based aminomutases in β-amino acid biosynthesis

Article abstract of DOI:10.1021/ja0762689

β-Amino acids are widely used building blocks in both natural and synthetic compounds. Aromatic β-amino acids can be biosynthesized directly from proteinogenic α-amino acids by the action of MIO (4-methylideneimidazole-5-one)-based aminomutase enzymes. Th

Full text of DOI:10.1021/ja0762689

Published on Web 12/05/2007
The Mechanism of MIO-Based Aminomutases in â-Amino Acid Biosynthesis
Carl V. Christianson,† Timothy J. Montavon,† Grace M. Festin,† Heather A. Cooke,†
Ben Shen,‡,§,| and Steven D. Bruner*,†
Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467,
Department of Chemistry, DiVision of Pharmaceutical Sciences, and UniVersity of Wisconsin National CooperatiVe
Drug DiscoVery Group, UniVersity of WisconsinsMadison, Madison, Wisconsin 53705
Received August 20, 2007; E-mail: bruner@bc.edu
â-Amino acids are important building blocks in a variety of
polymers and small molecules. 2,3-Aminomutases catalyze the
direct conversion of proteinogenic R-amino acids to â-amino acids.1
A subset of this enzyme class is dependent on the uncommon
cofactor 4-methylideneimidazole-5-one (MIO) and utilizes aromatic
R-amino acids as substrates.2 Natural product biosynthetic pathways
for enediynes, taxanes, and nonribosomal peptides contain MIO-
based aminomutases.2a,3 The X-ray structure of tyrosine aminomu-
tase from the enediyne C-1027 producer Streptomyces globisporus
(SgTAM) has recently been determined.4 The results established
that MIO-based aminomutases are structural homologues to am-
Figure 1. Mechanistic proposals for MIO-based enzymes.
monia lyases. The mechanism of MIO-based ammonia lyases has
been extensively studied; however, the role of the cofactor in the
chemistry is actively debated, and not entirely resolved.5 In general,
two mechanisms have been proposed for MIO-catalyzed elimination
of ammonia in R-amino acids. The primary obstacle the enzyme
overcomes is removal of a relatively nonacidic â-hydrogen. The
highly electrophilic cofactor has been postulated to react either with
the R-amino group (path a) or the aromatic ring (path b) to generate
Figure 2. (A) Synthesis and evaluation of SgTAM mechanistic probes:
the two covalent adducts shown in Figure 1 (1 or 4). Both pathways
(a) (R)-tert-butylsulfinimine, CsCO3, DCM; (b) Zn0, ethyl bromodifluoro-
acetate, THF; (c) 6N HCl, ∆; (d) i-PrOH, propylene oxide. (B) Concentra-
tion-dependent inhibition of SgTAM by 11.
lead to deprotonation and elimination (2 or 6) of ammonia to form
the conjugated olefin. On the basis of the high structural homology,
the mechanism of aminomutases is likely an extension of the lyase
chemistry with readdition of the amine via 1,4-conjugate addition.2,4
Supporting this mechanism, aminomutase activity has been deter-
mined to proceed through a cinnamate intermediate and is
reversible.2b
Any potential 2,3-aminomutase mechanism will proceed through
abstraction of the R- and â-hydrogens. To generate a stable mech-
anistic probe for SgTAM, we exploited â-Tyr analogues with
fluorine atoms substituted for the R-hydrogens. R,R-Difluoro-â-
tyrosine 11 provides an informative trapped mechanistic probe for
either of the two mechanistic scenarios. The analogue was
synthesized using chiral sulfinimine auxiliary chemistry starting
from TBS-protected 4-hydroxybenzaldehyde.6 To assess the capac-
ity of 11 to inhibit SgTAM, an HPLC-based assay was used to
determined the IC50.2 The results show enzyme inhibition in a
concentration-dependent manner with an IC50 of 970 µM (Figure
2B).
structural variations (rmsd over all atoms ) 0.71 Å). Electron
density corresponding to 11 is evident in the active site with density
continuous with the MIO cofactor (Figure 3A). Multiple conforma-
tions and binding possibilities for the inhibitor were evaluated,
focusing on adducts predicted by the two mechanisms shown in
Figure 1. Only the amine-bound adduct (corresponding to path a)
fit the density and the resulting bound-amine complex was fully
refined using simulated annealing and energy minimization. The
observed density does not match an MIO/phenyl ring adduct
consistent with a Friedel-Crafts mechanism, and the final model
places the MIO methylene carbon 3.4 Å from the meta-carbon of
the tyrosine ring. In addition, the observed binding mode is
consistent with the structure of an amino/phosphonate inhibitor
bound to tyrosine ammonia lyase.7 To further confirm the position
of 11 in the active site, R,R-difluoro-â-4-methoxyphenylalanine 12
was prepared and crystallized with SgTAM. By applying the
diffraction data from the cocomplex of 12 to the isomorphous
structure of 11-bound, electron density corresponding to the variant
methoxy group is easily observed. As shown in Figure 3C, the
difference map (Fo - Fc) of the methoxy adduct establishes the
position of the methyl group in 12 as consistent with our structural
assignment of the bound inhibitor. The methyl group is accom-
modated in the active site by displacing an ordered water molecule
(Figure 3A).
Cocrystals of 11 and SgTAM were prepared by incubation of
the analogue with the enzyme for 1 h at room temperature followed
by crystallization under conditions similar to those reported for the
apo-structure.4 The cocomplex structure was solved using molecular
replacement and refined to 2.0 Å resolution. Overall the structure
was very similar to the unliganded enzyme, with no significant
† Boston College.
‡ Department of Chemistry, University of Wisconsin.
§ Division of Pharmaceutical Sciences, University of Wisconsin.
| University of Wisconsin National Cooperative Drug Discovery Group,
University of Wisconsin.
The cocrystal structure of 11/SgTAM provides detailed insight
into the chemistry of the reversible 1,2 amino shift catalyzed by
SgTAM. The key substrate specificity determinants for the amino
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10.1021/ja0762689 CCC: $37.00 © 2007 American Chemical Society

C O M M U N I C A T I O N S
Figure 3. Structure of SgTAM bound to the substrate analogue 11. (A) Electron density map (2Fo - Fc at 1.5σ) showing the active-site region. The
inhibitor is shown in black and the MIO cofactor red. (B) Representation of the major interactions and conformation of the enzyme with the bound analogue.
(C) View of the active site showing the electron density map (Fo - Fc at 2.0σ) calculated from cocrystals of analogue 12 showing the position of the methyl
group.
acid are His93 and Tyr415. These two residues form a bifurcated
hydrogen bond with the substrate phenol (Figure 3AB). The residue
corresponding to His93 has been implicated as a key specificity
determinant in tyrosine and phenylalanine ammonia lyases.7,8 The
carboxylate of the amino acid forms hydrogen bonds with Arg311
and Asn205. Overall, the active site contains a high percentage of
aromatic residues. The MIO is stacked with Phe356 (not illustrated)
and Tyr308 is adjacent to the methylene of the MIO. Tyr63 is
positioned in close proximity to the R and â-carbons of the inhibitor
and is well-positioned to assist in the elimination chemistry. Gly70
forms a hydrogen bond with the phenol of Tyr63 and both residues
are conserved in all MIO-based lyases and mutases. Tyr63 and
Gly70 reside on a loop that is often disordered in unliganded
ammonia lyase crystal structures. The phenolic oxygen of Tyr63
is positioned 3.2 Å away from the R-carbon and 3.4 Å from the
â-carbon of the bound inhibitor. Tyr63, in the phenolate state, can
act as a general base (Figure 4), shuttling the proton between the
R- and â- positions. The pKa of Tyr63 needs to be lowered in the
active site of SgTAM to favor the anionic form. Two aspects are
evident from the structure that contribute to a lower pKa: (i)
stabilization of the negative charge by the backbone hydrogen bond
of Gly70 and (ii) the significant number of R-helices with positive
dipoles pointed at the active site both will favor the phenolate. Also
consistent with this mechanism, the measured optimal pH for
SgTAM is ∼9.2b To confirm the importance of Tyr63 in the reaction
mechanism, site-directed mutagenesis was used to remove the
phenol by substituting phenylalanine. The resulting mutant, Tyr63Phe,
had no measurable aminomutase activity up to 1.9 mM substrate
concentration (see Supporting Information).
MIO adduct. Modeling of this orientation shows the active site can
accommodate this change while still maintaining binding interac-
tions between Arg311, His93, and Tyr415.
The presented structures of the aminomutase SgTAM provide
strong evidence that MIO-based enzymes use covalent catalysis
through the R-amine to direct the chemistry. For ammonia lyases,
a covalent adduct orients both an enzymatic base and the leaving
group for an E2-type elimination. For enzymes with aminomutase
activity, the conjugate 1,4-addition into the relatively nonelectro-
philic 4-hydroxycinnamate is facilitated by orienting the amino-
bound intermediate and maintaining the nucleophile in the neutral
form. Differentiation of the two catalytic pathways can be ac-
complished by retention of ammonia in the closed active site of
aminomutases.4
Acknowledgment. This work is supported in part by funds from
Boston College and the Damon Runyon Cancer Research Founda-
tion DRS-41-01 (S.D.B.) and NIH Grants CA78747 and CA113297
(B.S.). We thank Dr. Y. Li, Institute of Medicinal Biotechnology,
Chinese Academy of Medical Sciences, Beijing, China, for the
C-1027-producing S. globisporus strain and A. Orville and the staff
at the Brookhaven NSLS PXRR for assistance with X-ray data
collection.
Supporting Information Available: Full experimental details for
synthesis and characterization of inhibitors, co-complex crystallization,
structure determination and biochemical characterization of inhibitors/
mutant enzymes. This material is available free of charge via the Internet
at http://pubs.acs.org.
References
The reaction of the related phenylalanine aminomutase has been
shown to proceed through stereospecific exchange of the proS
hydrogen.9 R-Tyr bound to MIO in a trans-configuration places
the proS hydrogen in proximity to Tyr63 and anti-periplanar to
the ammonium leaving group. The stereochemistry of the reverse
reaction of aminomutases (â-Tyr to R-Tyr) is variable. SgTAM
catalyzes the racemization of (S)-â-Tyr and a highly homologous
tyrosine aminomutase from chondramide biosynthesis produces the
opposite stereochemistry at the â-position, (R)-â-Tyr.3c The ster-
eochemical differentation can occur from rotation of the trans-
cinnamate intermediate to present the opposite face to the amine-
(1) (a) Wetmore, S. D.; Smith, D. M.; Radom, L. J. Am. Chem. Soc. 2001,
123, 8678-8689. (b) Lelais, G.; Seebach, D. Biopolymers 2004, 76, 206-
243.
(2) (a) Christenson, S. D.; Liu, W.; Toney, M. D.; Shen, B. J. Am. Chem.
Soc., 2003, 125, 6062-6063. (b) Christenson, S. D.; Wu, W.; Spies, M.
A.; Shen, B.; Toney, M. D. Biochemistry 2003, 42, 12708-12718.
(3) (a) Walker, K. D.; Klettke, K.; Akiyama, T.; Croteau, R. J. Biol. Chem.,
2004, 279, 53947-53954. (b) Jin, M.; Fischbach, M. A.; Clardy, J. J.
Am. Chem. Soc. 2006, 128, 10660-10661. (c) Rachid, S.; Krug, D.;
Weissman, K. J.; Mu¨ller, R. J. Biol. Chem. 2007, 282, 21810-21817.
(4) Christianson, C. V.; Montavon, T. J.; Van Lanen, S. G.; Shen, B.; Bruner,
S. D. Biochemistry 2007, 46, 7205-7214.
(5) (a) Poppe, L.; Retey, J. Angew. Chem., Int. Ed. Engl. 2005, 44, 3668-
3688. (b) Hermes, J. D.; Weiss, P. M.; Cleland, W. W. Biochemistry,
1985, 24, 2959-2967.
(6) (a) Staas, D. D.; Savage, K. L.; Homnick, C. F.; Tsou, N. N.; Ball, R. G.
J. Org. Chem., 2002, 67, 8276-8279. (b) Sorochinsky, A.; Voloshin, N.;
Markovsky, A.; Belik, M.; Yasuda, N.; Uekusa, H.; Ono, T.; Berbasov,
D. O.; Soloshonok, V. A. J. Org. Chem. 2003, 68, 7448-7454.
(7) Louie, G. V.; Bowman, M. E.; Moffitt, M. C.; Baiga, T. J.; Moore, B. S.;
Noel, J. P. Chem. Biol. 2006, 13, 1327-1338.
(8) Watts, K. T.; Mijts, B. N.; Lee, P. C.; Manning, A. J.; Schmidt-Dannert,
C. Chem. Biol. 2006, 13, 1317-1326.
(9) Mutatu, W.; Klettke, K. L.; Foster, C.; Walker, K. D. Biochemistry 2007,
46, 9785-9794.
Figure 4. Proposed mechanism for SgTAM activity.
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