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COMMUNICATION
Engineering the Amine Transaminase from Vibrio fluvialis
towards Branched-Chain Substrates
Maika Genz,[a] Okke Melse,[a] Sandy Schmidt,[a] Clare Vickers,[a] Tom van den Bergh,[b] Henk-Jan
Joosten,[b] and Uwe T. Bornscheuer*[a]
Abstract: Chiral amines are important building blocks, especially for
the pharmaceutical industry. Although amine transaminases (ATA)
are versatile enzymes to synthesize chiral amines, the wild-type
enzymes do not accept ketones with two large substituents next to
the carbonyl function. Using bioinformatic tools to design a 7-site
mutant library followed by high-throughput screening, we were able
to identify variants with a widened binding pocket of the enzyme
from Vibrio fluvialis (VF-ATA) as exemplified for a range of ketones.
Three variants allow the asymmetric synthesis of tert-butylphenyl
amine – not accessible by any wild-type ATA described so far. The
best variant containing four mutations (L56V, W57C, F85V, V153A)
gave 100% conversion of the ketone, yielding the amine with
>99%ee, notably with a preference to the (R)-enantiomer. In silico
modeling enabled the reconstruction of the substrate binding mode
to the newly evolved binding pocket and hence to explain the
experimental results.
side chain present in amino acids such as alanine, commonly
serving as amine donor, binding in the same pocket.[4] This dual
substrate recognition is realized by a flexible arginine residue,
called ‘flipping arginine’ (R415 in the enzyme from Vibrio
fluvialis; VF-ATA). This arginine is located in the large binding
pocket and either forms a salt bridge to the carboxylate group or
moves out of the active site (Figure 1A).
Chiral amines are versatile building blocks for the
pharmaceutical and agrochemical industry. Hence, methods for
their stereoselective synthesis are highly desired, especially to
ensure that the desired biologically active enantiomer is solely
produced. Beside the chemical asymmetric synthesis using
stereoselective hydrogenation with transition-metal catalysts and
enzymatic methods using e.g. imine reductases, amine
dehydrogenases or monoamine oxidases, amine transaminases
(ATA) have become an important alternative route for the
synthesis of chiral amines.[1] The most popular example for the
engineering of an ATA is the (R)-selective transaminase ATA117 developed by Merck & Co and Codexis, which contains 27
mutations to enable the biocatalytical production of the drug
sitagliptin.[2] Notably, this enzyme belongs to fold class IV,
whereas (S)-selective ATA belong to the structurally different
fold class I.
Transaminases are pyridoxal-5'-phosphate (PLP) dependent
enzymes.[3] The active form of transaminases is known to be a
homodimer with the active site at the dimer interface built up
from residues of both monomers. The substrate binding site of
ATAs is defined by a large and a small binding pocket (Figure 1).
The small binding pocket provides space for either the alkyl side
chain of the hydrophobic substrate or, alternatively, the acidic
[a]
[b]
Dr. M. Genz, O. Melse, Dr. S. Schmidt, Dr. C. Vickers, Prof. Dr. U.T.
Bornscheuer
Department of Biotechnology & Enzyme Catalysis
Institute of Biochemistry
Felix-Hausdorff-Str. 4
D-17487 Greifswald (Germany)
E-Mail: [email protected]
http://biotech.uni-greifswald.de
T. van den Bergh, Dr. H.-J. Joosten
Bio-Prodict
Nieuwe Marktstraat 54E
6511 AA Nijmegen (The Netherlands)
Supporting information for this article is given via a link at the end of
the document.
Figure 1. Substrate binding pocket of the ATA from Vibrio fluvialis (VF-ATA;
PDB-code: 4E3Q). A) Schematic view of the large and small binding pocket
bearing the external aldimine intermediate (PLP-Schiff' base with (S)-1phenylethylamine). The catalytic lysine (K285) is highlighted in red. The
targeted amino acids are colored (7-site library yellow, V153 green). The
asterisk denotes residues, which are located in the second monomer forming
the active site of the dimeric ATA. B) View of the substrate binding pocket.
Important residues are shown as sticks: Pyridoxamine-5’-phosphate (PMP) in
dark grey, 7-site library in yellow, V153 in green.
When considering the benchmark substrate for transaminases,
1-phenylethylamine (1b, Scheme 1), the phenyl group is placed
COMMUNICATION
in the large binding pocket whereas the small binding pocket is
mainly limited to a methyl group. In the past few years, a lot of
effort has been undertaken to engineer transaminases of fold
class I in such a way that the small binding pocket can accept
bulky moieties like an ethyl (Scheme 1, 2b), propyl (3b) or
ethanol side chain, albeit with limited success, especially if
larger substituents are present.[4b, 5] Recently, we have
succeeded in engineering the (S)-selective ATA from Ruegeria
sp. (pdb-code 3FCR) to enable the synthesis of a range of bulky
amines with high to excellent enantioselectivity. [6] For this
purpose only five mutations were required and to achieve
reasonable activity only two mutations (Y59W/T231A in 3FCR,
corresponding to W57/A228 in VF-ATA) were sufficient.
Interestingly, these two residues are present in wild-type VFATA, but this enzyme has no activity towards bulky substrates.
As VF-ATA is one of the most frequently used (S)-ATAs, this
lack of activity prompted us to subject this enzyme to extensive
protein engineering to make it capable to accept the bulky
substrates 3b–6b (Scheme 1) beyond the compounds
mentioned above – including 2b. Thus far the conversion of
branched chained substrates could not be achieved.[7] The only
exception is a variant of ATA-117, which gave 56% conversion
for phenylisobutylamine (4b).[2]
NH2
1b
NH2
4b
NH2
2b
NH2
5b
NH2
3b
NH2
6b
Scheme 1. Target amines for the iterative extension of the binding pocket of
the VF-ATA. The box highlights the motif, which binds in the small pocket.
To achieve this goal, our protein design strategy consisted of
three steps: (i) enlarging the volume of the substrate binding
pocket by creation of a library including mainly hydrophobic
residues in the active site, (ii) optimization of the hits for
asymmetric synthesis and (iii) combination of all findings to
create a synthetically useful final variant.
In order to identify most suitable mutation sites and amino
acid substitutions in the ATA from Vibrio fluvialis, we have
performed a bioinformatic analysis using 3DM. 3DM is a protein
superfamily analysis suite, which uses highly sophisticated
algorithms for the calculation of alignments based on
structure/sequence-function relationships
of
a defined
superfamily.[8] A database on the PLP-dependent transferases of
fold type I was used, which contains 725 structures to which
61,560 sequences were aligned.[3] Within this superfamily
database, a sub-dataset based on the VF-ATA (pdb-code:
4E3Q[5a]) was created with 12,956 aligned sequences. This
inspection identified seven positions (F19, L56, W57, F85, F86,
R415, and L417) within the binding pocket of VF-ATA – all
containing important hydrophobic residues involved in substrate
binding in the active site (Figure 1). These positions were then
subjected to mutagenesis using distinct degenerate codons
encoding hydrophobic amino acids selected based on the 3DM
analysis (Supporting Information, Table S9). Thereby the active
site is widened by the introduction of smaller hydrophobic amino
acids, while preserving the hydrophobic network, which is
important for the interaction of both monomers creating the
active site. After expression in E. coli, this 7-site library
comprising 16,384 mutations/combinations was screened at our
fully automated robotic platform (http://lara.uni-greifswald.de)
using rac-3b or rac-4b as amine donors in the kinetic resolution
mode.[9] Because the flipping arginine (R415) was included in
the library, screening was performed not only with pyruvate, but
also with pentanal as amine acceptor as this is only accepted if
the R415 is mutated.[5d] The screening of 2,240 variants (4.5%
coverage of the total library) already resulted in the identification
of five hits, which contained up to five mutations in the positions
L56, W57, F85, R415 and L417 (Supporting Information, Tables
S1 and S2). From these hits the variants H1 (L56V, W57F, F85V,
R415C) and H3 (L56V, W57C, R415F, L417A) were the most
active ones as both of them showed an increase in activity using
both amines 3b and 4b (Table 1 and Supporting Information,
Tables S3 and S4). Calculation of the binding pocket volume
indeed revealed the desired increase: the active site of H1 was
enlarged 1.4-fold (122 Å3) and for H3 3.1-fold (275 Å3) compared
to the wild type (88 Å3) (Supporting Information, Table S5).[10]
In the second screening round, conversion of the more
sterically demanding amines 5b and 6b was targeted. It was
known that the change of V153 to alanine is beneficial for the
conversion of bulky substrates.[5a,7] Therefore, the mutations
V153A and – to create even more space – V153G were
introduced into H1 and H3 resulting in H1_A or H1_G and H3_A
or H3_G, respectively (see Table S1 in the Supporting
Information for the nomenclature and mutations present in all
variants). Comparing the variants containing V153A or V153G, it
becomes obvious that the V153A mutation is beneficial (H1_A
shows a 12-fold increase in activity towards amine 4b compared
to H1; H3_A of about 2-fold) whereas the V153G mutation only
gave a 2-fold improvement over H1 and even a decrease in
activity using H3_G compared to H3 (Supporting Information,
Table S4). This can be attributed to the possible role of V153 in
dimer formation, which can also explain the loss in protein
stability for V153G (Supporting Information, Table S8 and Figure
S3).
At this point it was noticed that the change of the flipping
arginine R415 to either phenylalanine or cysteine lead to a loss
of activity in asymmetric synthesis using alanine as amine donor
(see Supporting Information). Thus, residue R415 was backmutated in variant H1 leading to H1_R and in H3 (including the
back-mutation of L417) leading to H3_R. We already showed
that position L417 does not have a positive effect when widening
the substrate binding pocket.[5d]
COMMUNICATION
Table 1. Specific activity (As) of the most important variants determined in kinetic resolution. Variants were tested with the corresponding amine using either
pyruvate or pentanal as amine acceptor. For determination of the activity all variants were produced in E. coli and purified.[5d]
Enzyme
As[a] [U mg-1]
As [U mg-1]
As [U mg-1]
As [U mg-1]
As [U mg-1]
As [U mg-1]
variant
pyruvate : 4b
pyruvate : 5b
pyruvate : 6b
pentanal : 4b
pentanal : 5b
pentanal : 6b
[b]
Wt
0.056 ± 0.008
n.a.
n.a.
0.045 ± 0.010
n.a.
n.a.
H1
0.104 ± 0.005
0.008 ± 0.002
n.a.
0.140 ± 0.011
0.054 ± 0.002
n.a.
H3
0.055 ± 0.009
n.a.
n.a.
0.118 ± 0.013
n.a.
n.a.
H1_A
0.064 ± 0.007
0.006 ± 0.001
n.a.
1.642 ± 0.048
0.055 ± 0.005
0.302 ± 0.013
H1_R
0.009 ± 0.005
0.013 ± 0.001
0.012 ± 0.002
0.063 ± 0.031
0.046 ± 0.003
n.a.
H3_A
0.077 ± 0.002
n.a.
0.009 ± 0.004
0.232 ± 0.028
0.030 ± 0.004
0.044 ± 0.020
H3_R
0.072 ± 0.007
0.012 ± 0.001
n.a.
0.077 ± 0.013
n.a.
n.a.
H3_RV
0.047 ± 0.007
0.0336 ± 0.0001
n.a.
0.081 ± 0.022
0.025 ± 0.001
n.a.
H3_RA
0.121 ± 0.015
0.0780 ± 0.0003
n.a.
0.127 ± 0.016
0.0235 ± 0.0009
n.a.
H3_RAV
0.181 ± 0.016
0.118 ± 0.003
0.036 ± 0.015
0.288 ± 0.067
0.067 ± 0.001
n.a.
[a] As = Specific activity where 1 U corresponds to 1 µmol product formation per min; [b] n.a.: not active / below detection limit; more detailed information about
all variants can be found in the supporting information in Table S3 (with pyruvate) and Table S4 (with pentanal) as amine acceptor.
Reconstruction of R415 in both variants does not have a positive
influence in kinetic resolution mode (Table 1), but in asymmetric
synthesis (Table 2). Comparison of all variants for amine 5b
revealed H1_R and H3_R as best variants (Table 1,
pyruvate:5b). Thus, we focused on the variants containing the
back-mutated R415 as only these can be used for asymmetric
synthesis with alanine. Calculation of the binding pocket volume
of the variants H1_R and H3_R resulted in 113 A³ and 175 A³,
respectively (Supporting Information, Table S5).[10] This finding
reveals that the W57C mutation in H3_R creates even more
space in the binding pocket compared to both mutations of
H1_R, W57F and F85V (L56V is present in both variants). The
specific activity for both variants concerning amine 5b and
pyruvate is almost equal, concerning 6b only H1_R shows some
minor activity (Table 1, pyruvate as acceptor).
Finally, the best two variants were combined for the creation
of a larger binding pocket: H3_R was used as template, as it has
a larger binding pocket than H1_R and can perform asymmetric
synthesis in contrast to H3. H3_R was complemented with either
the beneficial mutation of V153A (resulting in H3_RA) or the
hotspot from the variant H1, which is F85V (resulting in H3_RV)
or both (resulting in H3_RAV). All of these new variants showed
activity using amines 4b and 5b – with highest activity for the
H3_RAV variant (Table 1, pyruvate; 181 mU mg-1 for 4b and 118
mU for 5b). For the most interesting amine 6b, only the H3_RAV
variant showed activity (Table 1, pyruvate; 36 mU mg-1).
Interestingly, variant H1_R also showed activity with amine 6b
(Table 1, pyruvate; 12 mU mg-1). Variants H2, H3_A and H3_G
also showed some minor activity using 6b in kinetic resolution,
but as they still contained mutations at position R415, they were
not considered for asymmetric synthesis.
With these results achieved, we performed asymmetric
synthesis of 4b–6b using only the variants having the R415
intact (Table 2). From all variants, H1_R, H3_RA and H3_RAV
showed conversion for the targeted amines. Wild-type VF-ATA
gave only 6% conversion after 8d using 4a, and no conversion
at all for 5a and 6a. Again, for all three amines the H3_RAV
variant was the best enzyme resulting in 74% conversion for 4b,
87% conversion for 5b and full conversion of 6b, (for 6b notably
accomplished after only 48 h, Supporting Information Table S6).
Here, all active mutants gave the (R)-enantiomer with excellent
(99% ee) optical purity (Table 2). In case of 4b and 5b optical
purities were lower, but as our protein engineering strategy
targeted to find active enzyme variants, it is not surprising that
they might not exhibit also high enantioselectivity. A closer look
to the substrate binding revealed that 6b is more restrained to
the active conformation and thus fits better in the binding pocket
compared to amine 4b and 5b (Supporting Information, Table
S7).
Table 2. Asymmetric synthesis using wild-type ATA and the lead variants.
Substrate
Variant
4b
5b
6b
Conv.[a]
Optical
purity[b]
Conv.
Optical
purity
Conv.
Optical
purity
[%]
[%ee]
[%]
[%ee]
[%]
[%ee]
–
n.a.
–
[c]
[d]
Wt
6
n.d.
n.a.
H1_R
18
19
39
n.d.
77
> 99 (R)
H3_R
10
n.d.
n.a.
–
n.a.
–
H3_RV
4
n.d.
15
n.d.
n.a.
–
H3_RA
42
80
11
n.d.
25
> 99 (R)
H3_RAV
74
50[e]
87
> 13
100
> 99 (R)
[a] Conv. = conversion after 8 d (determined by GC) [b] ee = enantiomeric
excess, [c] n.d. = not determined [d] n.a. = not active or below detection limit,
[e] switch in enantiopreference compared to H1_R and H3_RV. Reaction
conditions and further details for asymmetric synthesis are given in the
Supporting Information (Table S6). It should be noted, that H1 and H3 were
not active in asymmetric synthesis, due to the mutation of R415(C/F).
COMMUNICATION
[6]
In summary, a combination of a ‘small, but smart’ library design
by 3DM-based bioinformatic analysis with in silico studies
resulted in the creation of variants of the amine transaminase
from Vibrio fluvialis, able to catalyze the asymmetric synthesis of
sterically demanding branched-chain chiral amines. Although
only activity was a design target, we were very pleased to find
that in case of tert-butylphenylamine also excellent optical purity
could be achieved.
Experimental Section
All experimental details are provided in the Supporting Information.
Acknowledgements
We thank the European Union (KBBE-2011-5, Grant No.
289350), the DFG (INST 292/118-1 FUGG) and the federal state
Mecklenburg-Vorpommern for financial support. We gratefully
acknowledge Byung-Gee Kim (Seoul National University, Seoul,
Korea) for providing the gene encoding the ATA from Vibrio
fluvialis, Dr. Hans Iding (Hoffman LaRoche Ltd., Basel,
Switzerland) for providing the pure enantiomer of (S)-6b, Dr.
Ingrid Costa for assistance during synthesis of amine 5b and Ina
Menyes for help during GC analysis. Additionally, we thank Prof.
Dr. Matthias Höhne (Greifswald University, Greifswald,
Germany) and Dr. Ioannis Pavlidis (Kassel University, Kassel,
Germany) for fruitful discussions.
Keywords: bioinformatics • chiral amines • enzyme catalysis •
protein engineering • transaminase
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COMMUNICATION
Entry for the Table of Contents
COMMUNICATION
Based on bioinformatic analysis
of the binding site of amine
transaminases, a 7-site
combinatorial library of the
enzyme from V. fluvialis was
created. High-throughput
screening of this library led to the
identification of enzyme variants
able to convert sterically
demanding ketones to afford the
corresponding chiral amines in
high to excellent optical purities
and yields.
M. Genz, O. Melse, S. Schmidt, C.
Vickers, T. van den Bergh, H.-J.
Joosten, U.T. Bornscheuer*
Page No. – Page No.
Engineering the Amine
Transaminase from Vibrio
fluvialis towards Branched
Chain Substrates