Spinosyns A and D (spinosad) are complex polyketide natural products biosynthesized through the cooperation of a modular polyketide synthase and several tailoring enzymes. SpnP catalyzes the final tailoring step, transferring forosamine from a TDP-D-forosamine donor substrate to a spinosyn pseudoaglycone acceptor substrate. Sequence analysis indicated that SpnP belongs to a small group of glycosyltransferases (GTs) that require an auxiliary protein for activation. However, unlike other GTs in this subgroup, no putative auxiliary protein gene could be located in the biosynthetic gene cluster. To learn more about SpnP, the structures of SpnP and its complex with TDP were determined to 2.50 and 3.15 Å resolution, respectively. Binding of TDP causes the reordering of several residues in the donor substrate pocket. SpnP possesses a structural feature that has only been previously observed in the related glycosyltransferase EryCIII, in which it mediates association with the auxiliary protein EryCII. This motif, H-X-R-X5-D-X5-R-X12-20-D-P-X3-W-L-X12-18-E-X4-G, may be predictive of glycosyltransferases that interact with an auxiliary protein. A reverse glycosyl transfer assay demonstrated that SpnP possesses measurable activity in the absence of an auxiliary protein. Our data suggest that SpnP can bind its donor substrate by itself but that the glycosyl transfer reaction is facilitated by an auxiliary protein that aids in the correct folding of a flexible loop surrounding the pseudoaglycone acceptor substrate-binding pocket.
Spinosyns A and D (spinosad) are complex polyketide natural products biosynthesized through the cooperation of a modular polyketide synthase and several tailoring enzymes. SpnP catalyzes the final tailoring step, transferring forosamine from a TDP-D-forosaminedonor substrate to a spinosyn pseudoaglycone acceptor substrate. Sequence analysis indicated that SpnP belongs to a small group of glycosyltransferases (GTs) that require an auxiliary protein for activation. However, unlike other GTs in this subgroup, no putative auxiliary protein gene could be located in the biosynthetic gene cluster. To learn more about SpnP, the structures of SpnP and its complex with TDP were determined to 2.50 and 3.15 Å resolution, respectively. Binding of TDP causes the reordering of several residues in the donor substrate pocket. SpnP possesses a structural feature that has only been previously observed in the related glycosyltransferase EryCIII, in which it mediates association with the auxiliary protein EryCII. This motif, H-X-R-X5-D-X5-R-X12-20-D-P-X3-W-L-X12-18-E-X4-G, may be predictive of glycosyltransferases that interact with an auxiliary protein. A reverse glycosyl transfer assay demonstrated that SpnP possesses measurable activity in the absence of an auxiliary protein. Our data suggest that SpnP can bind its donor substrate by itself but that the glycosyl transfer reaction is facilitated by an auxiliary protein that aids in the correct folding of a flexible loop surrounding the pseudoaglycone acceptor substrate-binding pocket.
Spinosyns A and D (9 and 10, respectively; termed spinosad) derived from Saccharopolyspora spinosa are the active ingredients of
commercial insecticides for the treatment of lice, fleas, and agricultural
pests.[1,2] Spinosyns are biosynthesized through the
action of a modular polyketide synthase (PKS) and several tailoring
enzymes, two of which are glycosyltransferases (GTs), SpnG and SpnP
(Figure 1).[3−6] They aid in spinosyn biosynthesis by attaching
rhamnose and forosamine sugars, critical for the biological activity
of spinosad, to the aglycone intermediates 3 and 4 and pseudoaglycone intermediates 7 and 8, respectively.[7,8]
Figure 1
Spinosad biosynthetic
pathway. SpnP is proposed to forosaminylate
intermediates 7 and 8 at 17-OH.
Spinosad biosynthetic
pathway. SpnP is proposed to forosaminylate
intermediates 7 and 8 at 17-OH.GTs generally deliver sugars from activated nucleotide
diphosphatesugardonor substrates to acceptor substrates.[9] These enzymes can be classified into more than 90 families, of which
family 1 (GT1) is the most common in the glycosylation of secondary
metabolites.[10,11] SpnG, whose crystal structure
was recently determined, belongs to the GT1 family.[12,13] Other members of GT1 family include the calicheamicin GT CalG1,
the erythromycin GT EryCIII, the oleandomycin GT OleD, the pikromycin
GT DesVII, the tylosin GT TylM2, the urdamycin GT UrdGT2, and the
vancomycin GT GtfA.[14−20] Each of these is an inverting GT-B enzyme (“inverting”
signifies that the stereochemistry at the anomeric position of the
product is the opposite of that of the TDP substrate; “GT-B”
denotes one of two principle glycosyltransferase folds) that transfers
a sugar from a UDP- or TDP-containing donor substrate to an aglycone
acceptor substrate in the biosynthesis of a natural product.[10]Sequence analysis reveals that SpnP is
also a member of the GT1
family. It catalyzes the attachment of forosamine (biosynthesized
from TDP-4-keto-6-deoxy-d-glucose by SpnN, SpnO, SpnQ, SpnR,
and SpnS) to 17-pseudoaglycone (7 and 8).[21] The in vivo activity of SpnP
has been established by gene deletion experiments; however, its in vitro activity has not yet been demonstrated.[4] Interestingly, SpnG and SpnP (25% identical sequences)
add sugars to similar substrates but display nearly opposite regiospecificities.
SpnG transfers rhamnose to the 9-OH of 3 and 4, while SpnP transfers forosamine to the 17-OH of 7 and 8. Thus, SpnG and SpnP must differentially orient similar
spinosyn carbon skeletons within their acceptor substrate-binding
sites.[16]A subset of GT1 enzymes,
including the GTs AknS, DesVII, EryCIII,
MycB, and TylM2, are known to require auxiliary proteins for their
catalytic activities.[17,22−26] These GTs often transfer deoxyaminosugars and are
encoded by a gene neighboring that of its auxiliary protein in the
biosynthetic cluster. A typical auxiliary protein possesses a P450
fold but lacks the conserved cysteine residue that serves as a ligand
to the hemeiron. These auxiliary proteins have a long, N-terminal
helix and are believed to be critical for the activation of their
cognate GTs. Thus far, the only available crystal structure of a GT
requiring an auxiliary protein is the binary complex of EryCIII with
its auxiliary protein, EryCII.[15]To complete the characterization of GTs involved in spinosyn biosynthesis,
we purified SpnP and demonstrated its in vitro activity
through a reverse glycosyl transfer assay. Crystal structures of SpnP
in its unliganded form and bound to the substrate donor analogue TDP
were also determined. On the basis of sequence and structure comparisons
with EryCIII and other GTs aided by auxiliary proteins, we hypothesize
SpnP requires an auxiliary protein for activation. Although the identity
of the auxiliary protein remains elusive, the SpnP structures reported
herein provide insight into a GT that is poised for pairing with an
auxiliary protein partner. These data add to the characterization
of the spinosyn biosynthetic pathway and illuminate the role of auxiliary
proteins in the activation of GTs.
Materials and Methods
Preparation
of Spinosyn A
Spinosad (9 and 10) was prepared from water/ethyl acetate (1:1) extractions
of Dow AgroSciences Tracer Naturalyte solutions. The pooled organic
fractions were washed with brine and concentrated.
Preparation
of 17-Pseudoaglycone
The 17-pseudoaglycone 7 was prepared as previously described.[27] Briefly, 1 N H2SO4 was added to spinosyn
A (9) and the mixture heated to 80 °C for 2 h. The
reaction mixture was cooled to room temperature, and the precipitate
was filtered, washed with 1 N H2SO4, and dissolved
in dichloromethane. The resulting solution was washed four times with
brine, dried over MgSO4, and concentrated.
Cloning, Expression,
and Purification of SpnP
The spnP gene was
amplified from genomic DNA of S. spinosa strain NRLL18537
and cloned into a pET28b(+) vector at the NdeI
and XhoI restriction sites. The forward primer 5′-AATAAGGCCATCGTGTCCTGTTCACC-3′
and reverse primer 5′-AACTCTCGAGTCACGGATGGCCATCAGAC-3′
were used for PCR amplification (restriction sites in bold and start
and stop codons in italics).The expression plasmid was then
transformed into Escherichia coli BL21(DE3). Overnight
cultures (LB with 50 μg/mL kanamycin, 5 mL) of the transformed
expression hosts were grown and used to inoculate 6 × 1 L cultures
(LB with 50 mg/L kanamycin). The cultures were incubated while being
shaken at 37 °C until the OD600 reached 0.6, after
which isopropyl β-d-thiogalactopyranoside (final concentration
of 0.5 mM) was added. The temperature was decreased to 15 °C,
and the cultures were grown for an additional 18 h. Cells were pelleted
via centrifugation (5000g for 10 min) and resuspended
in lysis buffer [5% (v/v) glycerol, 500 mM NaCl, and 30 mM HEPES (pH
7.5)] for sonication. Lysed cells were centrifuged (30000g for 30 min), and the lysate was loaded onto a Ni-NTA column (Qiagen).
Fifteen column volumes of 20 mM imidazole in lysis buffer was used
to wash the column before SpnP was eluted with 150 mM imidazole in
lysis buffer. SpnP was further purified over a gel filtration column
(Superdex 200, GE Healthcare Life Sciences) equilibrated with 5% (v/v)
glycerol, 150 mM NaCl, and 10 mM HEPES (pH 7.5). A protein concentrator
(Amicon, YM10 membrane) was used to achieve a concentration of 20
mg/mL. Aliquots were flash-frozen in liquid nitrogen and stored at
−78 °C until they were used further.
Crystallization,
Data Processing, and Structure Determination
Crystals of
SpnP were grown using the sitting-drop vapor-diffusion
method at 22 °C. The crystallization buffer consisted of 7 mM
17-pseudoaglycone 7, 46% (w/v) PEG 200, 0.6–3.0%
(w/v) dextran sulfate MR 5000, 0.2 M sodium chloride, and
0.1 M phosphate citrate buffer (pH 4.24). Each drop consisted of 2
μL of the SpnP protein solution (20 mg/mL) and 1 μL of
the crystallization solution with 500 μL of crystallization
buffer in the reagent reservoir. Crystals were flash-frozen in liquid
nitrogen prior to data collection. Crystals of SpnP complexed with
TDP were obtained by supplying 20 mM TDP (final concentration) to
the crystallization drop and incubating it for 1 h prior to flash-freezing.
Data for SpnP and the SpnP–TDP complex were collected at Advanced
Light Source beamlines 5.0.2 and 5.0.3, respectively, and processed
with HKL2000.[28] Molecular replacement was
utilized to determine the unliganded SpnP structure, using the EryCIII
monomer [Protein Data Bank (PDB) entry 2YJN] as the search model in Phaser.[29,30] The model was initially refined with ARP/wARP and built through
several rounds of refinement with Coot and Refmac.[31−33] ARP/wARP was
used to model in waters, which were then evaluated manually. The TDP
complex structure was determined by molecular replacement using the
unliganded SpnP structure.
Reverse Glycosyl Transfer Assay
The SpnP reverse glycosyl
transfer reaction mixture consisted of 100 μM spinosad (9 and 10), 1.0% (v/v) DMSO, 2.5 mM MgCl2, 2 mM TDP, 10 μM SpnP, and 100 mM HEPES (pH 8.0) (final volume
of 200 μL). Reaction mixtures were incubated for 16 h at 30
°C, after which 200 μL of ethanol was added. The resulting
mixtures were centrifuged (10000g for 5 min) to remove
debris, and samples were analyzed by high-performance liquid chromatography
(HPLC) with a C18 column (Varian): 80 to 90% B over 30
min [solvent A consisting of water and 20 mM ammonium acetate and
solvent B consisting of an acetonitrile/methanol mixture (50:50) and
20 mM ammonium acetate] at a 1 mL/min flow rate. Formation of 17-pseudoaglycone 7 was monitored at 254 nm and confirmed by mass spectrometry.
Results
Expression and Purification of SpnP
Attempts to express
and purify SpnP were problematic. Re-examination of the sequence of
the spnP gene and the flanking regions revealed that
its start codon likely resides at a region more downstream than that
originally assigned. The corrected open reading frame (ORF) is 48
bp shorter, corresponding to 16 fewer N-terminal residues. The truncated
construct begins with residues MRVL, more typical for GT-B enzymes.
Expression of this new construct yielded soluble protein. The numbering
of the residues in SpnP described here is based on the MRVL starting
sequence.
Crystallization and Structure Determination
In the
presence of 17-pseudoaglycone 7, crystals of SpnP were
observed within 2 weeks. In the absence of 7, crystals
appeared after 3 weeks but were smaller and did not diffract well.
The addition of dextran sulfate MR 5000 increased the crystal
size and quality. The EryCIII monomer (PDB entry 2YJN) was used as the
molecular replacement search model.[15] Unliganded
SpnP was refined to a resolution of 2.50 Å, and the SpnP–TDP
complex was refined to a resolution of 3.15 Å (Table 1).
Table 1
Data Collection and
Refinement Statistics
for SpnP and the SpnP–TDP Complex
SpnP
SpnP–TDP
Crystallization
Data
resolution (Å)
46.93–2.50 (2.56–2.50)
114.81–3.15 (3.23–3.15)
wavelength
(Å)
0.976
0.976
space group
P43212
P43212
a, b, c (Å)
162.4, 162.4, 81.2
162.4, 162.4, 81.3
no. of molecules
per asymmetric unit
2
2
no. of measured intensities
502778
274295
no. of unique reflections
71988
19214
completeness
(%)
99.7 (97.3)
99.0 (95.3)
Rsym
0.110
0.17
redundancy
7.0 (6.4)
14.3 (10.8)
average I/σI
49.3 (3.1)
16.7 (2.4)
Refinement
no.
of reflections
36239
18175
Rcryst/Rfree
0.203/0.257
0.209/0.314
no. of protein atoms
5772
5827
no. of ligand atoms
–
50
no. of solvent atoms
82
67
average B factor (Å2)
monomer A
63.1
62.7
monomer B
59.5
59.4
water
54.2
47.9
TDP
–
71.64
root-mean-square deviation
bond lengths (Å)
0.016
0.012
bond angles (deg)
1.956
1.814
Ramachandran
plot (%)
preferred
regions
93.94
87.70
allowed regions
3.17
7.38
outliers
2.89
4.92
Overall Structure of SpnP
SpnP is homodimeric with
W22 from each monomer forming a π-stacking interaction across
the 2-fold axis, a structural feature also observed in SpnG, CalG3,
and SsfS6[13,14,34] (Figure 2A). In addition, H414 makes a second stacking interaction
across the 2-fold axis of the SpnP dimer. The structure of the SpnP
monomer is consistent with the structural fold possessed by GT-B enzymes,
with two Rossmann-like domains, each containing a parallel β-sheet
with 321456 topology surrounded by α-helices.[9] The N-terminal domain consists of residues 1–224,
as well as residues 412–426 from the C-terminal helix, while
the C-terminal domain is comprised of residues 247–410. The
domains are linked by a long loop (residues 225–246). Two disordered
regions are present in each monomer, residues 63–98 and 261–271
in monomer A and residues 60–98 and 258–277 in monomer
B. The equivalent flexible loops of the nogalamycin GT SnogD have
been termed FL1 and FL2, respectively; thus, this nomenclature is
utilized here.[35] The active site is located
in a cleft between the N- and C-terminal domains with H13 likely serving
as the catalytic base (by analogy with other GT1 enzymes).
Figure 2
SpnP homodimer.
(A) Stereodiagram showing the asymmetric unit.
Asterisks mark the beginning and end of the first disordered loop
(FL1, residues 60–98). Diamonds mark the beginning and end
of the second disordered loop (FL2, residues 258–277). (B)
Stereodiagram of the donor substrate-binding site in the SpnP–TDP
complex showing the Fo – Fc omit map (contoured at 2.5 root-mean-square
deviations). The thymine base, deoxyribose, and the pyrophosphate
of TDP contact the labeled residues in the donor-binding site. (C)
Stereodiagram showing the SpnP active site in the absence of TDP (green)
and in the presence of TDP (gray). The TDP α-phosphate stabilizes
one conformation of the pyrophosphate-binding loop (H-X3-G-T motif), causing several residues to shift, notably H331 and
S333. Y315 also reorients to stack with the thymine base.
SpnP homodimer.
(A) Stereodiagram showing the asymmetric unit.
Asterisks mark the beginning and end of the first disordered loop
(FL1, residues 60–98). Diamonds mark the beginning and end
of the second disordered loop (FL2, residues 258–277). (B)
Stereodiagram of the donor substrate-binding site in the SpnP–TDP
complex showing the Fo – Fc omit map (contoured at 2.5 root-mean-square
deviations). The thymine base, deoxyribose, and the pyrophosphate
of TDP contact the labeled residues in the donor-binding site. (C)
Stereodiagram showing the SpnP active site in the absence of TDP (green)
and in the presence of TDP (gray). The TDP α-phosphate stabilizes
one conformation of the pyrophosphate-binding loop (H-X3-G-T motif), causing several residues to shift, notably H331 and
S333. Y315 also reorients to stack with the thymine base.
Donor Substrate-Binding Site
Similar
to other GT1 enzymes,
the donor substrate, TDP-d-forosamine, is expected to bind
to the C-terminal domain of SpnP. An α–β–α
motif (residues 315–343) constitutes the major portion of the
donor substrate-binding pocket (Figure 2B,C).
In the complex of SpnP with the donor substrate analogue TDP, the
thymine forms hydrophobic interactions with L254, Y315, and L318.
Several known GT1 enzymes that select TDP-linked sugars over UDP-linked
sugars (e.g., SpnG and SsfS6) contain an asparagine/threonine pair,
of which the asparagine NH2 forms a hydrogen bond with
the 3′-OH of the deoxyribose but sterically excludes UDP by
clashing with its 2′-OH.[13,34] Likewise, N230 and
T335 are present in SpnP, with the NH2 of N230 forming
a hydrogen bond with the 3′-OH of TDP. As with other structurally
characterized GT-B enzymes, an H-X3-G-T loop (H331–T336
in SpnP) contacts the pyrophosphate group of TDP through interactions
with the backbone NH groups (T335 and T336) and side chains (S11,
S12, H331, S333, T335, and T336). The binding of TDP causes several
residues to adopt conformations different from those in unliganded
SpnP. For example, Y315 reorders over the thymine to π-stack
with it and forms a hydrogen bond with the N230 backbone carbonyl
(similar interactions have been observed in other GTs)[14,16,20,36] (Figure 2C). In addition, the H331 side chain
reorients to form a charged hydrogen bond with the pyrophosphate group.
The sugar-binding motif in most GT1 enzymes, D/E-Q, which forms hydrogen
bonds with the sugar substituents, is replaced with D-E in SpnP (residues
356 and 357).[37]
Acceptor Substrate-Binding
Site
The binding site for
the 17-pseudoaglycone acceptor substrate (7 and 8) is principally formed by the N-terminal domain of SpnP
(Figure 2). Neither cocrystallization nor soaking
experiments with the 17-pseudoaglycone acceptor substrate 7 yielded the anticipated density. Soaking with spinosad (9 and 10) also did not yield new density. FL1 (also termed
the “specificity loop”) was invisible in the electron
density maps.[16] This region has been observed
to be structured in homologous GTs upon binding an acceptor substrate
and forms a large portion of the acceptor substrate-binding pocket;
however, it is often unstructured in the absence of an acceptor substrate.[13,14,16,35,38] Interestingly, most of FL1 in EryCIII forms
helices that make substantial contact with the auxiliary protein EryCII.
FL2 (residues 261–278), from the C-terminal domain, is also
in position to close over a bound acceptor substrate as observed for
CalG3 (PDB entry 3OTI).[14]
Three-Helix Motif
SpnP possesses a structural motif
that has been observed in only one other GT structure, EryCIII (Figure 3). This motif is comprised of three helices between
the fifth and sixth β-strands of the N-terminal domain. In EryCIII,
these helices, along with the helices of the structured FL1, form
the interface with the bound auxiliary protein EryCII. Significantly,
no structurally characterized GT1 apart from SpnP and EryCIII possesses
this motif. Because no other structurally characterized GTs require
an auxiliary protein for activity, the presence of this motif appears
to be a unique trait for a GT that pairs with an auxiliary protein.
Indeed, a sequence alignment shows that this motif exists in GT1s
known to require auxiliary proteins but is absent in GTs that act
alone to catalyze glycosyl transfer reactions (Figure 4). The alignment of the top 100 BLAST hits for SpnP reveals
a strong H-X-R-X5-D-X5-R-X12–20-D-P-X3-W-L-X12–18-E-X4-G
motif that begins in the fifth β-strand and ends before the
sixth β-strand of the N-terminal domain. Some of these highly
conserved hydrophobic residues (e.g., P179 and W183) are surface-exposed.
Other surface-exposed, hydrophobic residues in the motif include W159,
L160, F164, Y167, and F191. These residues are likely at the interface
formed between SpnP and its putative auxiliary protein. Several highly
conserved neighboring residues (e.g., W129 and T205 in SpnP) provide
structural support for the motif.
Figure 3
Auxiliary protein contact. (A) Complex
of the GT EryCIII (fuchsia)
with its auxiliary protein EryCII (light pink). (B) Structural alignment
of SpnP (green), SpnG (blue), and EryCIII (fuchsia). The putative
catalytic base of SpnP, H13, is labeled. EryCIII and SpnP contain
a three-helix motif as well as a long FL1 (however, in the SpnP structure,
FL1 is disordered). (C) SpnP modeled with the EryCIII FL1. (D) Modeled
dimeric interface between SpnP and an auxiliary protein.
Figure 4
GT1 sequence alignment and three-helix motif. (A) A long
FL1 and
the three-helix motif (between the fifth and sixth β-strands
of the N-terminal domain) distinguish GT1s aided by auxiliary proteins.
FL1 (*) and FL2 (ϕ) are the longest disordered regions of SpnP.
The D/E-Q motif, known to help bind the sugar of the donor substrate,
is often substituted with other residues. The secondary structure
is from SpnP. Accession numbers: SpnP, AAG23277; EryCIII, YP_001102993; MegCIII, CAC37820; DesVII, AAC68677; TylMII, CAA57472;
CosG, ABC00729; DnrS, AAD15267; SnogD, AAF01811; SpnG, AAG23268; UrdGT2, AAF00209; CalG3, AAM94798; OleD, ABA42119;
GtfA, AAB49292. (B) Stereodiagram of the three-helix motif showing the locations
of its most highly conserved residues (green).
Auxiliary protein contact. (A) Complex
of the GT EryCIII (fuchsia)
with its auxiliary protein EryCII (light pink). (B) Structural alignment
of SpnP (green), SpnG (blue), and EryCIII (fuchsia). The putative
catalytic base of SpnP, H13, is labeled. EryCIII and SpnP contain
a three-helix motif as well as a long FL1 (however, in the SpnP structure,
FL1 is disordered). (C) SpnP modeled with the EryCIII FL1. (D) Modeled
dimeric interface between SpnP and an auxiliary protein.GT1 sequence alignment and three-helix motif. (A) A long
FL1 and
the three-helix motif (between the fifth and sixth β-strands
of the N-terminal domain) distinguish GT1s aided by auxiliary proteins.
FL1 (*) and FL2 (ϕ) are the longest disordered regions of SpnP.
The D/E-Q motif, known to help bind the sugar of the donor substrate,
is often substituted with other residues. The secondary structure
is from SpnP. Accession numbers: SpnP, AAG23277; EryCIII, YP_001102993; MegCIII, CAC37820; DesVII, AAC68677; TylMII, CAA57472;
CosG, ABC00729; DnrS, AAD15267; SnogD, AAF01811; SpnG, AAG23268; UrdGT2, AAF00209; CalG3, AAM94798; OleD, ABA42119;
GtfA, AAB49292. (B) Stereodiagram of the three-helix motif showing the locations
of its most highly conserved residues (green).
Activity Assays
The SpnPdonor substrate, TDP-d-forosamine, is very unstable, readily losing its TDP substituent.
Because of the difficulty of preparing sufficient amounts of TDP-d-forosamine to assay SpnP-catalyzed forosaminylation of 17-pseudoaglycone 7 directly, the activity of SpnP was analyzed in the reverse
direction.[39] Formation of 17-pseudoaglycone 7 was monitored in the assay mixture containing SpnP, superstoichiometric
TDP, and spinosad (primarily 9) under the reverse glycosyl
transfer conditions (Figure 5). A small quantity
of 7 could be detected only when SpnP was present in
the reaction conditions. Addition of auxiliary proteins for other
GTs, such as EryCII and DesVIII, had no effect on the reaction (see
the Supporting Information).
Figure 5
Reverse glycosyl
transfer assay. SpnP-mediated formation of 17-pseudoaglycone 7 from spinosyn A (9) and superstoichiometric
TDP was observed by reversed-phase HPLC (λ = 254 nm). Only when
SpnP and TDP were added to 9 was 7 produced
[confirmed by HRMS (see Figure S1 of the Supporting
Information)].
Reverse glycosyl
transfer assay. SpnP-mediated formation of 17-pseudoaglycone 7 from spinosyn A (9) and superstoichiometric
TDP was observed by reversed-phase HPLC (λ = 254 nm). Only when
SpnP and TDP were added to 9 was 7 produced
[confirmed by HRMS (see Figure S1 of the Supporting
Information)].
Discussion
Among the growing number of GTs characterized in vitro, at least five have been demonstrated to be aided
by an auxiliary
protein: EryCIII, CosG, DnrS, MegCIII, and DesVII. The presented structural
and bioinformatics analyses of forosaminyltransferase SpnP, which
catalyzes the final transformation in the biosynthesis of spinosad
(spinosyns A and D, 9 and 10, respectively),
indicate that SpnP is likely a new member of this subset of GTs requiring
an auxiliary protein for optimal activity. The only other GT in this
subset that has been structurally characterized is EryCIII, which
was observed to bind to its auxiliary protein EryCII in the absence
of substrates.A comparison of the structures of SpnP and EryCIII
clearly reveals
the resemblance of these two proteins. Half of the EryCIII–EryCII
interface is formed by helices located between the fifth and sixth
β-strands of the N-terminal subdomain. A similar three-helix
structural motif is also present in SpnP. A sequence alignment of
the top 100 BLAST hits for SpnP shows a high degree of conservation
for this motif with the consensus sequence H-X-R-X5-D-X5-R-X12–20-D-P-X3-W-L-X12–18-E-X4-G.[40] This motif is present
in GTs known to be aided by auxiliary proteins and may be a prognostic
trait of such GTs. Interestingly, SpnP can bind TDP by itself, suggesting
that the SpnP homodimer can bind the donor substrate TDP-d-forosamine without the aid of its auxiliary protein. TDP is bound
by SpnP in much the same way as it is bound by SpnG, with the diphosphate-binding
site reconfiguring.[13] In view of its ability
to form a complex with TDP and its N230/T339 motif, SpnP is expected
to be selective for TDP-linked sugars. A glutamate replaces a glutamine
in the second position of the D/E-Q motif observed in most GT-B enzymes;
the negatively charged residues, D356 and E357, may form ionic interactions
with the positively charged tertiary amine of the forosamine sugar
(Figure 6).
Figure 6
Model of the SpnP ternary complex. (A)
TDP-d-forosamine
and 17-pseudoaglycone 7 (PSA) were placed using the SpnP–TDP
complex structure. The dimethylamine moiety of the forosamine sugar
is in the proximity of the D356 and E357 carboxylates (the altered
“D/E-Q motif”). PSA is positioned to make hydrophobic
interactions with residues such as F354 and W355. The permethylated
rhamnose is pointed away from the active site, while 17-OH is adjacent
to the catalytic base, H13, and the electrophilic forosamine C1. (B)
SpnP forosaminylation. H13 is proposed to abstract a proton from 17-OH,
which nucleophilically attacks C1 of TDP-d-forosamine to
displace TDP and form spinosyn A (9).
Model of the SpnP ternary complex. (A)
TDP-d-forosamine
and 17-pseudoaglycone 7 (PSA) were placed using the SpnP–TDP
complex structure. The dimethylamine moiety of the forosamine sugar
is in the proximity of the D356 and E357 carboxylates (the altered
“D/E-Q motif”). PSA is positioned to make hydrophobic
interactions with residues such as F354 and W355. The permethylated
rhamnose is pointed away from the active site, while 17-OH is adjacent
to the catalytic base, H13, and the electrophilic forosamine C1. (B)
SpnP forosaminylation. H13 is proposed to abstract a proton from 17-OH,
which nucleophilically attacks C1 of TDP-d-forosamine to
displace TDP and form spinosyn A (9).Although the reverse glycosyl transfer assay presented
here demonstrates
that SpnP possesses measurable activity in the absence of an auxiliary
protein, it is relatively weak. Binding with its auxiliary protein
may facilitate the proper folding of SpnP and thereby improve its
catalytic efficiency. In the EryCIII–EryCII complex, FL1 is
structured into helices that make significant contact with EryCII.
Similarly, binding with an auxiliary protein may help order FL1 in
SpnP. The closed, structured loop would then be more organized for
binding the 17-pseudoaglycone acceptor substrate. Indeed, when the
17-pseudoaglycone is docked into the SpnP structure, the rhamnosesugar is positioned by FL1. An interaction between rhamnose and FL1
may help orient the substrate so that the 17-OH is placed next to
the active site base H13.Genes encoding auxiliary proteins
have been found only in gene
clusters encoding aminosugar-bearing metabolite biosynthesis and are
typically located directly upstream of the gene of the GT responsible
for the transfer of the amino sugar. However, the spinosyn biosynthetic
gene cluster does not contain a gene encoding an auxiliary protein
homologous to EryCII, AknT, DesVIII, TylM3, or MydC, for SpnP. Several
GTs requiring auxiliary proteins are known to be activated by noncognate
auxiliary proteins,[41] so SpnP could be
activated by an auxiliary protein encoded by a gene in a different
region in the S. spinosa genome. However, the P450-related
proteins identified through a BLAST search of the S. spinosa proteome using EryCII as the query all possess the cysteine residue
that is important for heme coordination and do not contain an unusually
long N-terminal extension. Lacking both signature features of GT-activating
auxiliary proteins, these P450-related proteins are unlikely candidates
to be the auxiliary protein for SpnP.In summary, the structure
of SpnP, an aminosugar GT in the spinosyn
biosynthetic pathway, was determined. The resemblance of its structure
to that of EryCIII provides a strong argument for the participation
of an auxiliary protein in SpnP-catalyzed glycosylation. If so, the
structure of SpnP represents the second example of GTs whose catalysis
is aided by an auxiliary protein. Several key hydrophobic residues,
highly conserved in the three-helix motif observed in GTs aided by
auxiliary proteins, are surface-exposed in SpnP and may play roles
similar to those of their counterparts within EryCIII in binding an
auxiliary protein. While the identity and function of the putative
auxiliary protein for SpnP remain to be determined, the results presented
here will impact the characterization and application of this group
of GTs important in the tailoring of biologically active secondary
metabolites.
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