Structure of a bacterial glycoside hydrolase family 63 enzyme in complex with its glycosynthase product, and insights into the substrate specificity

Authors


Abstract

Proteins belonging to glycoside hydrolase family 63 (GH63) are found in bacteria, archaea and eukaryotes. Although the eukaryotic GH63 proteins have been identified as processing α-glucosidase I, the substrate specificities of the bacterial and archaeal GH63 proteins are not clear. Here, we converted a bacterial GH63 enzyme, Escherichia coli YgjK, to a glycosynthase to probe its substrate specificity. Two mutants of YgjK (E727A and D324N) were constructed, and both mutants showed glycosynthase activity. The reactions of E727A with β-d-glucosyl fluoride and monosaccharides showed that the largest amount of glycosynthase product accumulated when galactose was employed as an acceptor molecule. The crystal structure of E727A complexed with the reaction product indicated that the disaccharide bound at the active site was 2-O-α-d-glucopyranosyl-α-d-galactopyranose (Glc12Gal). A comparison of the structures of E727A–Glc12Gal and D324N–melibiose showed that there were two main types of conformation: the open and closed forms. The structure of YgjK adopted the closed form when subsite −1 was occupied by glucose. These results suggest that sugars containing the Glc12Gal structure are the most likely candidates for natural substrates of YgjK.

Database

The coordinates and structure factors for E727A–Glc12Gal and D324N–melibiose have been deposited in the Protein Data Bank under accession numbers 3W7W and 3W7X, respectively

Abbreviations
AaGA

Aspergillus awamori glucoamylase

BhRex

Bacillus halodurans reducing-end xylose-releasing exo-oligoxylanase

GH

glycoside hydrolase family

Glc12Gal

2-O-α-d-glucopyranosyl-d-galactopyranose

Sf GA

Saccharomycopsis fibuligera glucoamylase

WT

wild-type

β-GlcF

β-d-glucopyranosyl fluoride

Introduction

Proteins belonging to glycoside hydrolase family 63 (GH63) are found in bacteria, archaea and eukaryotes. The eukaryotic GH63 proteins have been identified as processing α-glucosidase I (EC 3.2.1.106), which specifically hydrolyzes the terminal α-1,2-glucoside linkage of Glc3Man9GlcNAc2, an oligosaccharide precursor of N-linked glycoproteins [1-4]. The subsequent steps of metabolism, including removal of the two α-1,3-linked glucose residues by processing α-glucosidase II, and further modification by various glycosidases and glycosyltransferases, produce a wide variety of N-glycosylated proteins. Therefore, processing α-glucosidase I is a key enzyme for regulation of N-linked oligosaccharide processing in eukaryotic cells [5, 6]. Many bacteria and archaea, which do not produce the eukaryotic-type N-glycans [7], also are reported to possess genes for GH63 proteins. However, unlike the eukaryotic GH63 proteins, the physiological functions and substrate specificities of the bacterial and archaeal proteins are not clear.

We previously reported the crystal structure and some enzymatic properties of a bacterial GH63 enzyme, Escherichia coli YgjK [8]. Although YgjK is a member of the GH63 family in the CAZy classification database (http://www.cazy.org) [9], its homology to the eukaryotic processing glucosidases is low. The overall sequence identity between YgjK and Saccharomyces cerevisiae processing α-glucosidase I [10] is 12%. The enzymatic activity of YgjK for commercially available sugars was highest for the α-1,3-glucosidic linkage of nigerose [Glc-α(1→3)-Glc]. However, the Km value for nigerose (230 ± 90 mm) was substantially higher than that for other typical α-glucosidases, which suggests that nigerose is not the natural substrate for YgjK [8]. The structure of YgjK consists of two domains, the N-domain and the catalytic A-domain, joined by a linker region. The N-domain comprises a super-β-sandwich, and the A-domain formed an (α/α)6 barrel. An extra structure, the A’-region (residues 441–567), is present in the A-domain, and comprises four α-helices and five β-strands. Recently, the crystal structure of S. cerevisiae processing α-glucosidase I has been reported [11], and was found to have a similar fold, comprising the N-terminal super-β-sandwich domain and the (α/α)6 barrel catalytic domain [11]. The A-domain shares structural similarity with clan GH-G (GH37 [12] and GH63) and clan GH-L (GH15 [13-15], GH65 [16] and GH125 [17]) enzymes. The crystal structures of YgjK complexed with the monosaccharides glucose (Glc), mannose (Man) and galactose (Gal) revealed that all three monosaccharides are bound in the active site. Thus, the results did not clarify the substrate specificity for YgjK [8].

The GH63 proteins are inverting enzymes as shown by an NMR study [5]. Recent reports have shown that inverting glycosidases may be converted into glycosynthases [18-21]. Glycosynthases are engineered glycoside hydrolases that catalyze the synthesis of glycosides from activated donors, such as glycosyl fluorides or glycosyl azides [22-25]. A GH8 enzyme, reducing-end xylose-releasing exo-oligoxylanase from Bacillus halodurans (BhRex), is an inverting glycosidase that has the (α/α)6 barrel fold [26] and may be converted to a glycosynthase [18, 19]. Because GH63 enzymes have been suggested to be evolutionarily related to GH8 enzymes [27], YgjK is predicted to be able to be converted to a glycosynthase. Here, we describe conversion of the bacterial enzyme YgjK to the glycosynthase, and probe its substrate specificity.

Results and Discussion

Glycosynthase activity of E727A

Three conserved carboxylic amino acid residues (Asp324, Asp501 and Glu727) were identified in the active site of YgjK [8]. Asp501 and Glu727 are expected to act as the catalytic acid and base residues, respectively [8]. The conversion of BhRex to the glycosynthase has been extensively studied [18, 19]. In BhRex, the catalytic base residue Asp263 was modified, and the mutant showed glycosynthase activity [18]. Here, we replaced Glu727 of YgjK with Ala, and the mutant E727A was expressed in E. coli and purified. Hydrolytic activity of E727A for nigerose was not detected.

The glycosynthase activity of E727A for a mixture of β-d-glucopyranosyl fluoride (β-GlcF) and Glc was tested first, because the α-1,3-linked glucose disaccharide nigerose was the best substrate among the commercially available sugars. The reaction mixture was analyzed by TLC. In this reaction, most β-GlcF was hydrolyzed to form Glc, but a spot corresponding to a disaccharide was observed on TLC (Fig. 1A). The reactions of E727A with β-GlcF and the monosacchrides Man and Gal were then tested (Fig. 1B,C). In all reactions, spots corresponding to glycosynthase products were found, although most β-GlcF was degraded to produce Glc. The largest amount of glycosynthase product accumulated when Gal was employed as an acceptor molecule. The reaction mixtures containing acceptor monosaccharides other than Glc, Man and Gal were also analyzed (Fig. S1), and the accumulations of glycosynthase products derived from them were lower than those derived from Gal.

Figure 1.

Glycosynthase activity of YgjK E727A and D324N. Glycosynthase-derived products are indicated by asterisks. (A–C) TLC analysis of the glycosynthase reaction of E727A using a mixture of β-GlcF (donor) and Glc (A), Man (B) or Gal (C) (acceptor). (D–F) Glycosynthase reaction patterns of E727A and D324N for a mixture of β-GlcF (donor) and Gal (D), lactose (E) or melibiose (F) (acceptor). (G) Two-dimensional TLC analysis of the hydrolytic activity of the WT enzyme for the glycosynthase product Glc12Gal. Lanes: R, reaction products of E727A with a mixture of β-GlcF and Gal; M, malto-oligosaccharide markers comprising glucose to maltopentaose (G1–G5).

Glycosynthase activity of D324N

The mutant BhRex Y198F was reported to show glycosynthase activity [19]. The mutated residue, Tyr198, was adjacent to the catalytic base residue Asp263, which has been proposed to act as a nucleophilic water holder [26, 28]. Although no residue equivalent to Tyr198 of BhRex was found in the active site of YgjK, the aspartate residue Asp324 is widely conserved in the active sites of clan GH-G and GH-L enzymes, and this residue is located at the bottom of the subsite −1 pocket (subsite numbering according to Davies et al. [29]). We reported the crystal structure of wild-type (WT) YgjK complexed with Man (WT–Man) [8]. In this structure, a Man molecule was present at subsite −1 (Man –1), and Asp324 directly formed hydrogen bonds with atom O6 of Man –1. Two water molecules, designated W1 and W2 (labeled Wat1138 and Wat1306 in Mol-A and Wat1205 and Wat1263 in Mol-B, in the coordinate PDB 3W7T, WT–Man), formed hydrogen bonds with atom OE1 of Glu727. W1 also interacted with atom O6 of Man –1 via hydrogen bonds (Fig. 2A). It is likely that one of the water molecules is a nucleophile. Asp324 appeared to interact indirectly with the nucleophilic water through atom O6 of Man –1. In this study, Asp324 was replaced by Asn, and the hydrolytic and glycosynthase activities of D324N were tested. Enzymatic activity of D324N for nigerose was not observed.

Figure 2.

Candidates for the nucleophilic water. Two water molecules are found to interact with catalytic base Glu727 in the structures of WT–Man (A) (PDB ID 3W7T) and WT–Glc (B) (PDB ID 3W7S). The 2 Fo − Fc electron density maps of the water molecules are contoured at 1.0 σ.

A mixture of β-GlcF and Gal was incubated with E727A or D324N, and the reactions were analyzed by TLC. The reaction pattern of D324N was essentially identical to that of E727A (Fig. 1D). The disaccharides lactose and melibiose, which contain a Gal residue, were incubated as acceptor substrates under the same conditions, and the reactions were analyzed by TLC. New spots corresponding to glycosynthase products were found on the TLCs for both reactions (Fig. 1E,F). It is likely that these products were trisaccharides formed by transfer of a Glc residue from β-GlcF to a Gal residue of lactose or melibiose, and the spot intensities corresponding to these glycosynthase products were almost identical to those for β-GlcF and Gal. The results suggest that the YgjK glycosynthases prefer the Gal residue as an acceptor substrate.

Structure of E727A complexed with the reaction product

To determine the structure of the reaction product of YgjK E727A for a mixture of β-GlcF and Gal, and to elucidate the mechanism of glycosynthase activity, the crystal structure of E727A complexed with the reaction product was determined. A mixture of β-GlcF, Gal and E727A was incubated, the reaction product was isolated by preparative TLC, and approximately 4.8 mg of the purified product was obtained. A crystal of E727A was soaked in a solution containing the reaction product (approximately 15% w/v), and the structure of E727A complexed with the reaction product was determined at 2.0 Å resolution.

The asymmetric unit of the crystal contained two copies of the E727A complex, Mol-A and Mol-B. The electron density (2 Fo − Fc) maps for both copies contoured at 1 σ showed continuous density for almost all amino acid residues (residues 1–759 for Mol-A; residues 1–760 for Mol-B). After the initial structural refinement, clear electron density (Fo − Fc) maps for a disaccharide comprising Glc and Gal were observed at the active site of both Mol-A and Mol-B. Based on the electron density, the disaccharide bound at the active site was identified as 2-O-α-d-glucopyranosyl-α-d-galactopyranose [Glc-α(1→2)-Gal (Glc12Gal)] (Fig. 3A). 1H- and 13C-NMR were also performed to identify the glycosynthase product, and the values of chemical shifts were consistent with those reported for synthesized Glc12Gal [30]. These results indicate that YgjK E727A catalyzes transfer of β-GlcF to the 2-OH group of Gal (Fig. S2).

Figure 3.

Structures of the active sites of E727A–Glc12Gal (A) and D324N–melibiose (B). Glc12Gal, melibiose and amino acid residues interacting with Glc12Gal are shown using stick models, and colored in light blue, orange and yellow, respectively. Hydrogen bonds are indicated by black dashed lines. A magnesium ion bound to the catalytic acid Asp501 is colored green. The difference Fourier maps are calculated excluding the ligands, and the resulting Fo − Fc omit maps are contoured at 2.0 σ. (C) Structural comparison between E727A–Glc12Gal and D324N–melibiose. Amino acid residues interacting with the ligands are colored cyan (E727A–Glc12Gal) and yellow (D324N–melibiose). Glc12Gal and melibiose are shown in light blue and orange, respectively.

To test whether WT YgjK hydrolyzes Glc12Gal, two-dimensional TLC was performed. The mixture obtained from the reaction of β-GlcF, Gal and E727A was developed in the first direction, and the WT enzyme (1.0 mg·mL−1 YgjK in 100 mm sodium acetate buffer, pH 5.0) was sprayed on the TLC plate and incubated for 1 h at 35 °C, and then redeveloped in the second direction (Fig. 1G). The result indicates that Glc12Gal is hydrolyzed by YgjK to yield Glc and Gal.

Structural comparisons of D324N–melibiose and E727A–Glc12Gal

For further analysis of the substrate specificity of YgjK, the crystal structure of the mutant D324N complexed with melibiose (D324N–melibiose) was determined at 2.7 Å resolution. The D324N–melibiose complex crystallized in the same space group (P21) as the E727A–Glc12Gal complex, with almost identical cell parameters (Table 1). A continuous density for almost all amino acid residues was observed in D324N–melibiose (residues 1–760 for Mol-A; residues 1–760 for Mol-B). The following descriptions are based primarily on Mol-A, unless otherwise stated.

Table 1. Data collection and refinement statistics
 E727A–Glc12GalD324N–melibiose
  1. a

     The values for the highest-resolution shells are given in parentheses.

Data collection
BeamlinePF AR-NW12APF AR-NW12A
Wavelength (Å)1.01.0
Space groupP21P21
Cell dimensions
a (Å)58.962.1
b (Å)138.1138.2
c (Å)82.586.2
β (°)99.098.4
Resolution range (Å)50–2.00 (2.06–2.00)a50–2.70 (2.77–2.70)a
Measured reflections323 564111 834
Unique reflections86 82438 773
Completeness (%)100.0 (100.0)a98.0 (97.9)a
I/σ (I)19.6 (4.1)a20.2 (4.9)a
R merge 0.103 (0.413)a0.116 (0.343)a
Refinement statistics
R work 0.1740.189
R free 0.2260.249
RMSD
Bond lengths (Å)0.0100.007
Bond angles (°)1.201.13
Number of atoms
Protein12 16712 162
Ligand4646
Metal ion92
Water869150
Mean B values (Å2)
Protein23.125.2
Ligand18.236.2
Metal ion30.919.6
Water26.113.7

The structures of the E727A–Glc12Gal and D324N–melibiose complexes were compared. In E727A–Glc12Gal, a Glc12Gal molecule (mean B values of 19.4 Å2 for Mol-A and and 17.0 Å2 for Mol-B) was observed at subsites −1 to +1 (Fig. 3A). In the D324N–melibiose complex, the electron density for an α-melibiose molecule (mean B values of 32.9 Å2 for Mol-A and 39.5 Å2 for Mol-B) was found at subsites +1 to +2 (Fig. 3B). Superposition of the three structures showed that Glc, Gal and Glc residues were present at subsites −1, +1 and +2, respectively. These sugar residues were labeled Glc −1, Gal +1 and Glc +2. The positions of Gal +1 residues in these complexes were almost identical (Fig. 3C). The interactions between YgjK and these sugar residues were analyzed. There were many hydrogen bonds between YgjK and Glc –1, and also between YgjK and Gal +1. However, no direct hydrogen bonds formed between YgjK and Glc +2 in D324N–melibiose, which suggests that YgjK specifically interacted with the Glc −1 and Gal +1 sugar residues. It should be noted that a magnesium ion originating from the crystallization buffer solution was found adjacent to Asp501 in E727A–Glc12Gal (Fig. 3A). We tested whether the hydrolysis of nigerose by YgjK was affected by 10–100 mm MgCl2, but no effect was found (data not shown). The result suggests that binding of the magnesium ion may be an artifact of the crystallization process.

Although the crystal of D324N–melibiose diffracted to only moderate resolution (2.7 Å), the comparison suggested that Asn324 of D324N–melibiose may adopt a different conformation than Asp324 of E727A–Glc12Gal (Fig. 3C). The two water molecules W1 and W2, which are candidates to act as the nucleophilic water, were located near Glu727 and Man –1 in the structure of WT–Man (Fig. 2A). The two water molecules were found at the same positions in WT–Glc (labeled Wat1314 and Wat1328 in Mol-A, and Wat1462 and Wat1464 in Mol-B, in the coordinate PDB 3W7S), despite the fact that no ligand was present at subsite −1 (Fig. 2B). In both WT–Man and WT–Glc, Asp324 indirectly interacted through several hydrogen bonds with W1 and W2. A mutant of the nucleophilic water holder, D263N of BhRex, was reported to show glycosynthase activity, and the side chain of Asn263 had a different conformation than that of WT Asp263 [28]. It was impossible to determine the positions of water molecules in D324N–melibiose due to the low resolution of the data, but a similar mechanism is likely to operate in the acquisition of glycosynthase activity by YgjK D324N.

YgjK is structurally homologous to GH15 glucoamylases. Structures of glucoamylases from Aspergillus awamori and Saccharomycopsis fibuligera (AaGA and SfGA, respectively) in complexes with the maltotetraose analog acarbose have been determined, and an aspartic acid residue corresponding to Asp324 of YgjK (Asp55 in AaGA; Asp70 in SfGA) formed hydrogen bonds with atoms O4 and O6 of the valienamine residue at subsite −1 of acarbose [14, 31]. Atom O6 of the valienamine residue interacted with OE1 of the catalytic general base residue (Glu400 in AaGA; Glu456 in SfGA) via a water molecule, which was thought to act as a nucleophile. The kinetic properties of WT and mutants of AaGA were reported, and the kcat values for D55G showed a 200-fold decrease for maltose and a 300-fold decrease for maltoheptaose compared to those of WT, whereas the Km values of D55G were similar to those of WT. Therefore, Asp55 was thought to be involved in the hydrolytic transition state rather than ground-state binding [32]. Similarly, SfGA D70N lost hydrolytic activity for soluble starch [33]. These results indicate that Asp324 of YgjK plays a similar role in substrate binding and the hydrolytic reaction.

An open-to-closed conformational change of YgjK

Comparison of the structures showed that there were two distinct conformations, designated here as open and closed forms, in the A-domain of YgjK, and the structures of D324N–melibiose and E727A–Glc12Gal were identified as the open form and closed form, respectively. The width of the active-site pocket was narrowed in the closed form (Fig. 4A). The Cα backbone of the A-domain of E727A–Glc12Gal was compared with that of D324N–melibiose using the program DynDom [34] in the CCP4 suite [35], and nine bending regions (residues 290–291, 307–310, 321–325, 327–328, 330–331, 333–334, 442–443, 554–562 and 580–597) were identified (shown in green in Fig. 4A,B). The conformational change appeared to be centered on three bending regions (residues 442–443, 554–562 and 580–597). The A-domain was roughly divided into three modules: module 1 (residues 274–441 and 563–579), module 2a (residues 444–553; part of the A’-region) and module 2b (residues 580–760) (Fig. 4B), and module 2a and module 2b were seen to move together. For the whole A-domain, the root mean square deviation (for CA atoms) between E727A–Glc12Gal and D324N–melibiose was 0.939 Å, whereas those for module 1, module 2a and module 2b were 0.579, 1.37 and 0.365 Å, respectively. Although the value for module 2a was high due to the flexibility of the A’-region, module 1 and module 2b behaved as rigid bodies. We previously determined the structures of WT–Glc (in which the sugar molecules were bound at subsites +1 and +2), WT–Man (in which the sugar molecules were bound at subsites −1 and +1) and WT–Gal (in which the sugar molecule was bound at subsite +1) [8], and all were identified as the open form.

Figure 4.

Conformational changes in the catalytic domain of YgjK. (A) Comparison of the Cα backbones of E727A–Glc12Gal (closed form: module 1, red; modules 2a and 2b, blue) and D324N–melibiose (open form: module 1, pink; modules 2a and 2b, cyan). The bending regions are shown in green. Glc12Gal is shown as a black stick-and-ball model. (B) Domain movement analysis of the A domain using DynDom [34], showing module 1 (red), module 2a (cyan), module 2b (blue), the bending regions (green) and Glc12Gal (black). (C–E) Comparison of the active sites of (C) WT–Man (semi-open form, Mol-A, magenta) and E727A–Glc12Gal (semi-closed form, Mol-A, light blue), (D) D324N–melibiose (fully open form, Mol-A, orange) and WT–Man (semi-open form, Mol-A, magenta), and (E) Mol-A of E727A–Glc12Glc (semi-closed form, yellow) and Mol-B of E727A–Glc12Gal (fully closed form, blue). Symbols: dashed line, hydrogen bond; arrow, movement during the conformational change. In (E), Glu727 and the W1 water molecule in WT–Man are shown in red for clarity.

We superposed the structures of E727A–Glc12Gal (closed form) and WT–Man (open form). These structures were determined at high resolution (2.0 and 1.5 Å, respectively). Subsite −1 was occupied by Glc (Glc –1) and Man (Man –1), respectively. The structural comparison showed that the two loops move on binding to Glc –1, and the catalytic acid residue Asp501 points towards the active-site pocket (Fig. 4C and Fig. S3A,C). d-Glucopyranose is the C2 epimer of d-mannopyranose, and the position of atom O2 appeared to be critical for the conformational change. Atom O2 of Man –1 was unable to interact with the side chain of Asp501 in WT–Man (open form), whereas atom O2 of Glc –1 formed a hydrogen bond with atom OD1 of Asp501 in E727A–Glc12Gal (closed form) (Fig. 4C). The distance between atom CA of Asp501 and atom C2 of Man –1 in WT–Man (open form) was 7.2 Å, whereas the distance between atom CA of Asp501 and atom C2 of Glc –1 in E727A–Glc12Gal (closed form) was 6.4 Å. Due to this narrowing of the active-site pocket, atom OD2 of the catalytic acid residue Asp501 formed a hydrogen bond with the glycosidic linkage oxygen atom of Glc12Gal. A similar movement was observed for Trp680, a residue located adjacent to Asp501, and this movement also contributed to narrowing of the active-site pocket (Fig. 4C and Fig. S3A,C). Atom NE1 of Trp680 did not interact with Man −1 directly in WT–Man (open form), whereas NE1 formed a hydrogen bond with atom O2 of Glc −1 in E727A–Glc12Gal (closed form). The residue corresponding to Trp680 was highly conserved among the GH63 proteins, and was found in a Y-W-R-X-X-X-W motif (X = any residue; the tryptophan residue corresponding to Trp680 is underlined) [8].

These results suggest that YgjK is an enzyme that hydrolyzes sugars containing a Glc-α(1→2)-Gal structure. Although Man was able to bind to subsite −1, the WT–Man structure adopted an open form, indicating that subsite −1 was specific for Glc. Glc, Man and Gal were observed at subsite +1 [8]. However, the position and orientation of the hexose rings of Glc and Man were different from that of Gal, and only Gal at subsite +1 appeared to form a glycosidic linkage with Glc –1. The sugar Glc12Gal has been found to be attached to various collagens from vertebrates [36-38], and therefore YgjK may participate in degradation of collagens to produce an energy source for the gut bacterium E. coli. Further studies, such as a kinetic study using Glc12Gal, are required to determine whether Glc12Gal is the natural substrate for YgjK.

Two open forms and two closed forms of YgjK

A further comparison of the structures indicated that there were two open forms and two closed forms in the A-domain of YgjK (Fig. 4D,E and Fig. S3). The backbone conformations of D324N–melibiose and WT–Man, both of which adopted the open form, were essentially identical. However, the side chain of Trp323 in D324N–melibiose pointed away from the active-site pocket, whereas atom NE1 of Trp323 in WT–Man formed hydrogen bonds with atoms O3 and O4 of Man −1 due to the conformational change of Trp323 (Fig. 4D and Fig. S3C,D). The results indicate that the conformational change in Trp323 was accompanied by ligand binding at subsite −1, and the structures of D324N–melibiose and WT–Man were designated as fully open and semi-open forms, respectively. The residue corresponding to Trp323 was fully conserved among bacterial GH63 enzymes.

In the closed form, the conformations of the two residues in the vicinity of subsite −1 (Tyr679 and Arg683) in Mol-A of E727A–Glc12Gal were different from those of Mol-B (Fig. 4E and Fig. S3A,B). The side chain of Tyr679 in Mol-A did not form any hydrogen bonds (semi-closed form). In Mol-B, the side chains of Tyr679 and Arg683 were oriented toward the active site, and atom OH of Tyr679 interacted with a water molecule through a hydrogen bond (fully closed form). If the mutation of Glu727→Ala is not introduced, atom OE1 of Glu727 may be located at the position of this water molecule (designated W3 in Fig. 4E and labeled Wat1309 in Mol-B of the coordinate E727A–Glc12Gal), and atom OH of Tyr679 may form a hydrogen bond with atom OE1 of the catalytic base residue Glu727. The conformational changes of Tyr679 and Arg683 were probably induced during the enzymatic reaction. The residue corresponding to Tyr679 was widely conserved among GH63 enzymes, and the residue corresponding to Arg683 was found among some bacterial GH63 enzymes. These observations suggest that the four forms (fully open, semi-open, semi-closed and fully closed) are sequentially processed. However, it is unclear whether this process occurs, because semi-open and semi-closed forms were found in WT complexed with the unnatural substrate Man and the mutant enzyme E727A, respectively.

To our knowledge, this is the first demonstration of an open-to-closed conformational change among the two structurally related clans GH-G and GH-L. It would be interesting to determine whether similar conformational changes are induced in other GH-G and GH-L enzymes. Recently, two bacterial GH63 proteins from Thermus thermophilus HB27 and Rubrobacter radiotolerans have been characterized and identified as mannosylglycerate hydrolases [39]. They hydrolyze the α-1,2-linkage of mannopyranosyl-α(1→2)-glycerate and glucopyranosyl-α(1→2)-glycerate, both of which accumulate in response to salt stress in archaea and bacteria. The crystal structure of a T. thermophilus HB8 protein, which has 99% sequence homology with T. thermophilus HB27 mannosylglycerate hydrolase and 17% sequence homology with the catalytic domain of YgjK, has been determined (PDB ID 2Z07). Superposition of the T. thermophilus HB8 protein and YgjK E727A–Glc12Gal indicates that the amino acid residues forming subsite +1 are not fully conserved, although the amino acid residues comprising subsite −1 are fully conserved (Fig. 5). Asp368 and Lys391 in YgjK, interacting with atom O4 of Gal +1, correspond to His71 and Gln103, respectively, in the T. thermophilus HB8 protein. This may result in the substrate specificity differences between YgjK and mannosylglycerate hydrolases. Additional studies are required to elucidate the relationships between conformational changes and substrate specificities of clan GH-G and GH-L enzymes.

Figure 5.

Structural comparison between YgjK and T. thermophilus mannosylglycerate hydrolase. Amino acid residues forming subsites −1 to +1 of YgjK and mannosylglycerate hydrolase are colored in yellow and blue, respectively. Glc12Gal is represented by a black line.

Experimental procedures

Synthesis of β-d-glucopyranosyl fluoride

β-d-glucopyranosyl fluoride tetraacetate was synthesized as described by Hall et al. [40]. β-GlcF was prepared by deacetylation of 40 μmol tetraacetate in 1 mL methanol mixed with 5 μL 1 m sodium methoxide/methanol solution, incubated at room temperature for 30 min, and followed by evaporation. The reaction product was stored at −20 °C and dissolved in water just before use.

Preparation of YgjK mutants

Standard DNA manipulations were performed as described by Sambrook et al. [41]. Escherichia coli strains JM109 and BL21 (DE3) were used for DNA manipulation and protein expression, respectively. Site-directed mutagenesis was performed using a QuikChange site-directed mutagenesis kit (Agilent Technologies, Santa Clara, CA, USA) with expression plasmid pYgjK-SIG [42] as the template. To construct expression plasmids for mutants D324N and E727A, the oligonucleotides 5′-CAGACCTGGCCGTGGAATACCTGGAAGCAG-3′ and 5′-GATGGACCAATTCAGGCAAATTACAACCCGCTGAC-3′, respectively, and their complementary strands were used as primers. WT and mutant proteins were expressed and purified as described previously [8]. Briefly, crude enzymes produced in E. coli BL21 (DE3) cells harboring the desired plasmid were purified by hydrophobic interaction chromatography (HiPrep 16/10 Phenyl FF High-Sub column; GE Healthcare, Chalfont St Giles, UK), anion-exchange chromatography (HiLoad 16/10 Q-Sepharose HP column; GE Healthcare), and gel-filtration chromatography (HiPrep 26/60 Sephacryl S-200 HR column; GE Healthcare). The purity of the proteins was analyzed by SDS/PAGE. Protein concentration was determined by measuring the absorbance at 280 nm based on theoretical molar absorption coefficients calculated using ExPASy ProtParam (http://web.expasy.org/protparam/).

Measurement of enzymatic activity

Nigerose (Hayashibara Biochemical Laboratories, Okayama, Japan) was used for measurement of hydrolytic activity. Twenty microliters of YgjK in 10 mm Tris/HCl buffer (pH 7.5) and 80 μL of 23 mm nigerose in 100 mm sodium acetate buffer (pH 5.0) were mixed and incubated at 35 °C for 30 min. The reaction was quenched by mixing with an equal volume of 0.5 m sodium carbonate solution (pH 10.0). The amount of Glc released was assayed using the mutarotase/glucose oxidase/peroxidase method performed using a Glucose CII-Test Wako kit (Wako Pure Chemical Industries, Osaka, Japan). One unit was defined as the amount of enzyme that produced 1 μmol Glc from nigerose per min.

Analysis of the glycosynthase reaction

To analyze the glycosynthase reaction, Glc, Man, Gal, d-fructose, d-xylose, l-arabinose, l-fucose, lactose [Gal-β(1→4)-Glc] and melibiose [Glc-α(1→6)-Glc] were used as acceptor substrates. The glycosynthase activity of the WT and mutant enzymes was examined by incubating the reaction mixtures containing 100 mm sodium phosphate buffer (pH 7.0), 50 mm β-GlcF, 50 mm acceptors and 5 mg·mL−1 enzymes in a total volume of 40 μL at 35 °C for 1 h, followed by heat treatment at 95 °C for 5 min. The reaction products were analyzed by TLC using a silica gel 60 glass plate (Merck, Darmstadt, Germany). The plate was developed in a mixture of 1-butanol/ethanol/water (5 : 5 : 2 by volume), and the spots were detected by heating after spraying with 5% sulfuric acid/methanol solution. The reaction product obtained from E727A for a mixture of β-GlcF and Gal was isolated by preparative TLC. A mixture of β-GlcF (150 μmol) and Gal (150 μmol) was prepared in 100 mm sodium phosphate buffer (pH 7.0, 2.5 mL), E727A (0.5 mL, 30 mg·mL−1) was added, and the reaction was incubated at 35 °C for 16 h. The reaction product was isolated using a silica gel 60 preparative TLC plate (Merck) under the conditions described above. NMR spectra (1H and 13C) of the product were obtained in D2O at 298 K using a Bruker Avance 800 spectrometer (Bruker Biospin, Rheinstetten, Germany), with 2-methyl-2-propanol as an internal standard.

Crystallization, data collection, and structure determination

The crystals of E727A and D324N mutants were grown at 20 °C using the hanging-drop vapor diffusion method, in which 1.0 μL of the protein solution (20 mg·mL−1) in 10 mm Tris/HCl buffer (pH 7.5) was mixed with an equal volume of a crystallization reservoir solution containing 15–20% w/w polyethylene glycol 8000 and 0.2–0.6 m magnesium chloride in 100 mm Tris/HCl buffer (pH 6.0–6.6). The crystals of the mutants were soaked with the well solution containing 30% w/v of the desired sugar, which also was used as a cryoprotectant. The diffraction data were collected at 100 K using the PF AR-NW12A beamline (Photon Factory, Tsukuba, Japan). All data were processed and scaled using HKL2000 [43]. The structure of the complex was solved by the molecular replacement method using MOLREP [44] in the CCP4 suite [35]. A model of YgjK complexed with mannose (PDB ID 3W7T) was used as a search model. Refinement was performed using REFMAC5 [45] in the CCP4 suite [35], and manual adjustment and rebuilding of the model were performed using COOT [46]. Solvent molecules were introduced using ARP/wARP [47]. Validation of the structures was performed using RAMPAGE [48] in the CCP4 suite [35]. Figures were prepared using PyMOL (http://www.pymol.org/). Data collection and refinement statistics are listed in Table 1. In Ramachandran plots, 95.6–97.2% of the residues were shown to be in the favored regions, and no residues were identified as outliers. The coordinates and structure factors for E727A–Glc12Gal and D324N–melibiose have been deposited in the Protein Data Bank under accession codes 3W7W and 3W7X, respectively.

Acknowledgements

We thank Tomoko Fujii for technical assistance. We also thank the staff of the Instrumental Analysis Center for Food Chemistry of National Food Research Institute for recording NMR spectra. This work was supported in part by a Grant-in-Aid for Scientific Research (number 23570132) to T.T., and a Research Fellowship from the Japan Society for the Promotion of Science to T.M. We also thank Hayashibara Co. Ltd for providing various sugars. This research was performed with the approval of the Photon Factory Advisory Committee, National Laboratory for High Energy Physics, Tsukuba, Japan (project number 2012G006).

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