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https://doi.org/10.1016/j.bbrc.2019.01.021
0006-291X/© 2019 Elsevier Inc. All rights reserved.
P. Kaila et al. / Biochemical and Biophysical Research Communications 509 (2019) 892e897 893
both amylase (Amy) and glucanotransferase (GT) functions] and encoding the wild-type PfuAmy (or PfuAmyGT), and incorporating
attempt to explore whether the two activities are derived from the mutations by encoding them in suitable forward and reverse
same site (or set of sites), or from entirely different sites. primers for each mutant (as listed below) and using these in
Glucanotransferases transfer small sugar units between glucans, splicing by overlap extension (SOE) polymerase chain reactions
causing donors to become shorter and acceptors to become longer. (PCR) to create the mutated full-length genes according to standard
If products remain competent to act as substrates (donors/accep- SOE-PCR protocols [18,19], followed by cloning into vector, pET-23a,
tors) in further cycles of activity, glucanotransferases can transform between restriction enzymes sites, NdeI and XhoI, and transforming
a homogenous population of a single glucan into a pool of glucans into XL1-Blue cells for propagation, or BL21 Star(DE3)pLysS cells for
of different lengths. A glucanotransferase must possess a glycoside expression and purification.
bond hydrolyzing function, as well as a glycoside bond synthesizing PfuAmyGT full-length F: 50 AATAATCATATGATCAATGGTTGG
function, whereas an amylase may possess only the former. ACC30
How are these functions coordinated? Since no crystal structure PfuAmyGT full-length R: 50 AATAATCTCGAGACCAGACGCTTC30
is available for PF0272, we turned to a homolog of known structure Pfu D362A F: 50 GCAACGCCGCGTACTG30
from T. litoralis [O32462 MALQ_THELN, UNIPROT], to use it as a Pfu D362A R: 50 CGTTGCGGCGCATGAC30
basis for comparative structural-bioinformatics studies, performing Pfu W365A F: 50 GACGCGTACGCGCACGGTCTG30
homology-based modeling, and exploring functional mechanisms Pfu W365A R: 50 CTGCGCATGCGCGTGCCAGAC30
through site-directed mutagenesis. We present an evidence-based Pfu H366A F: 50 GCGTACTGGGCCGGTCTGTTC30
hypothesis regarding locations of donor and acceptor sites, nature Pfu H366A R: 50 CGCATGACCCGGCCAGACAAG30
of glucose transfer, and a loop performing the transfer, containing a
catalytically-important residue (Asp362) and a glucose- 2.4. Immobilized metal affinity chromatographic (IMAC)
transferring residue (Trp365). purification
2. Material and methods Primary (10 ml) LB cultures expressing PfuAmyGT mutants were
grown in 100 mg/ml ampicillin and 35 mg/ml chloramphenicol, at
2.1. Materials 37 C, with shaking (220 rpm) for 12e16 h, and used for inoculation
of secondary (1000 ml) cultures grown to an O.D600 of 0.6, before
Malto-oligosaccharides were purchased from Santa Cruz addition of inducer (IPTG) to a final concentration of 1 mM, followed
Biotechnology, USA. Isopropyl-1-thio-D-galactopyranoside (IPTG) by growth for a further 6e7 h. Cells were harvested through centri-
was purchased from BR Biochem Life Sciences Pvt. Ltd, Delhi, India. fugation at 8000 rpm, re-suspended in non-denaturing pH 8.0 lysis
Restriction enzymes, DNA polymerase, and DNA ligase were pur- buffer (Qiagen) containing 10 mM Tris, 50 mM NaH2PO4 and 300 mM
chased from New England Biolabs (MA, U.S.A.). TLC silica gel 60 NaCl. Cells were sonicated and the lysate was heated at 90 C for
F254 plates were procured from Merck, New Jersey, USA. Kits for 15e20 min, to denature and heat-aggregate proteins (barring ther-
plasmid isolation, agarose gel DNA extraction, and PCR clean-up mostable PfuAmyGT and its mutants) and precipitate and sediment
were obtained from Qiagen, Germany. them through centrifugation at 12,000 rpm for 1 h. The PfuAmyGT/
mutant-enriched supernatant was subjected to affinity chromatog-
2.2. Comparison and analysis of modeled PfuAmyGT structure to a raphy on Ni-NTA resin per standard (Qiagen) protocols, using 1 ml
known homolog columns. Eluted protein was dialyzed in pH 8.0 Tris buffer (50 mM)
and examined on SDS-PAGE by the protocol of Laemmli [20], on a
The structure of PfuAmyGT was modeled using the software, I- Mini-Protean Tetrad apparatus (Bio-Rad, Richmond, CA, USA).
TASSER [13], and visualized using the software, PyMol [14]. This
structure was compared by both sequence-alignment (Clustal 2.5. Determination of oligomeric status
Omega) [15] and structure alignment (PyMol and TM align) [16] to the
known structure of a T. litoralis homolog (PDB IDs: 1K1X, 1K1Y, and Purified PfuAmyGT and its mutants were subjected to gel
1K1W). Surfaces, topologies, and secondary structures were filtration (size exclusion) chromatography on a Superdex-200 In-
compared through superimposition of known and predicted struc- crease 10/300 GL column, on an AKTA Purifier 10 chromatographic
tures. PDB IDs: 1K1X and 1K1Y show the T. litoralis homolog in system (GE Healthcare), using a flow rate of 0.5 ml/min, with the
complex with acarbose and maltose of unknown origin. We separated column pre-equilibrated with pH 8.0 Tris buffer (50 mM).
the coordinates of the two subunits of the T. Litoralis and P. furiosus
enzymes into four separate files, with bound acarbose/maltose where 2.6. Determination of secondary structural content
applicable, and superimposed all subunit structures to derive the
geometry of acarbose and maltose bound to the same subunit. Circular dichroism (CD) spectroscopy was performed on a
Chirascan spectropolarimeter (Applied Photophysics) fitted with a
2.3. Cloning and expression of PfuAmyGT mutants, D362A, W365A, peltier unit. A quartz cuvette of 0.1 cm path-length was used to
and H366A collect far-UV CD spectra (197e250 nm). Mean residual ellipticity
(MRE) was calculated using the following equation, where the
The PfuAmyGT protein has already described (PfuAmy) in a mean residue weight (MRW) was determined by dividing the
previous publication [17]. The desired mutants of the enzyme were molecular weight of the protein (in Da) by the number of amino
created by using (as template) the synthetic, codon-optimized gene acids in its polypeptide chain:
‘surface’ representation. distances). A suitable mechanism for such movement would require
From Fig. 1B, it becomes immediately evident that acarbose (in a moveable sub-structure capable of changing conformation, e.g., a
blue) and maltose (in pink) continue to remain placed next to each loop akin to those reported in other glycosyltransferases, in which
other. We also performed docking of acarbose and maltose with the tryptophan residues bind and carry the excised glucan [22]. We
predicted PfuAmyGT structure to verify that these binding sites and searched the vicinity of the acarbose and maltose binding sites for
orientations are preferred (data not shown). The acarbose appears such a loop and found a 15 residues-long loop constituting residues
to be buried in a tunnel. The maltose is bound to a groove. The two 361e375 of PfuAmyGT. In Fig. 1D, the loop is shown (in yellow) lying
PfuAmyGT subunits are also subtly different in structure. Small immediately below, and between, the reducing end of the putative
region(s) of non-overlap of structure show up in green in Fig. 1B (as (acarbose-bound) donor site and the non-reducing end of the pu-
these are not fully hidden by the overlapping subunit in red). tative (maltose-bound) acceptor site, with enough space sur-
Otherwise, this visualization manifests a model for maltose and rounding it to allow for conformational changes (all-atom
acarbose bound to chain A of PfuAmyGT. Chain B of PfuAmyGT was visualization not shown). Loop 362e375 contains a tryptophan
then deleted, leaving only chain A, acarbose and maltose, as shown (W365) which could be involved in glucan transfer, and an aspartate
in Fig. 1C, in which the structure of the region is also shown as a (D362) which could participate in the hydrolysis required to release
‘cut-out’. The non-reducing end of the maltose is next to the the glucose moiety from the donor. We mutated D362, W365, and
reducing end of acarbose (i.e., from the end of acarbose which H366 (another potentially important residue) to alanine.
would qualify to be called ‘reducing’, if it were maltotetraose). The
two molecules are so close to each other that is it conceivable that 3.3. Enrichment-cum-purification of PfuAmyGT mutants
PfuAmyGT could ‘clip’ off a glucose unit from maltotetraose (acting
as donor), and add it to maltose (acting as acceptor), to perform a Mutations Asp362Ala, His365Ala, and Trp366Ala were intro-
disproportionation reaction. If instead, the excision of glucose from duced and confirmed by Sanger sequencing. Fig. S2 shows the
maltotetraose were to occur without transfer to maltose, the alignment of PfuAmyGT and mutant protein sequences. PfuAmyGT
glucose could be released into solution, qualifying PfuAmyGT and the three mutants were purified by heating protein-expressing
(Pf0272) to function both as an amylase as reported by the group of E. coli cells at 90 C for 20 min, as described in the materials and
Christian B. Anfinsen [2], but notably only as an exo-amylase and methods. The SDS-PAGE analyses of these is shown in Fig. 2A,
not as an endo-amylase, and also as a glucanotransferase, as re- establishing purity and identical (correct) chain lengths.
ported by the group of Michael W. W. Adams [12].
For glucanotransferase activity, the excised glucose unit would 3.4. Structural-biochemical characterization of PfuAmyGT
need to be physically moved from the donor glucan (maltotetraose)
to the acceptor glucan (maltose), over a distance of some ~14e15 Å, Quaternary structure. Gel filtration chromatographic analyses are
as can be seen in Fig. 1D (which also shows certain other measured shown in Fig. 2B. These confirm that PfuAmyGT and its three mutants
Fig. 2. Characterization of PfuAmyGT and mutants. (A) SDS PAGE of heat- and affinity-purified ~78 kDa PfuAmyGT (lane 1), D362A (lane 2), molecular weight marker (lane 3),
H366A (lane 4), and W365A (lane 5). Some samples have undergone proteolysis to generate a ~52 kDa band and lower species during purification, but the segments remain
associated and folded, yielding a single peak in gel filtration. (B) Gel filtration chromatograms of PfuAmyGT and mutants. (C) CD spectra of PfuAmyGT and mutants. (D) Fluorescence
emission spectra of PfuAmyGT and mutants.
896 P. Kaila et al. / Biochemical and Biophysical Research Communications 509 (2019) 892e897
Fig. 3. Thermal stability of PfuAmyGT and mutants. Temperature-dependence of MRE (222 nm) values in CD spectra of (A) PfuAmyGT, and (B) its mutants (D362A, W365A, and
H366A).
Appendix A. Supplementary data hydrolase family 57 and identification of catalytic residues in amylopullula-
nase from Thermococcus hydrothermalis, Eur. J. Biochem. 271 (2004)
2863e2872.
Supplementary data to this article can be found online at [11] C.S. Rye, S.G. Withers, Glycosidase mechanisms, Curr. Opin. Chem. Biol. 4
https://doi.org/10.1016/j.bbrc.2019.01.021. (2000) 573e580.
[12] H.S. Lee, K.R. Shockley, G.J. Schut, S.B. Conners, C.I. Montero, M.R. Johnson,
C.J. Chou, S.L. Bridger, N. Wigner, S.D. Brehm, F.E. Jenney, D.A. Comfort,
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