CHAPTER 3 IN SILICO ANALYSIS OF SBP……………………………….. 40-72
3.3 RESULTS AND DISCUSSION
3.3.3 Trehalose/Maltose ABC transporter
each protein are provided in parenthesis. The analysis suggests the grouping of these proteins into three distinct clusters shown in blue (xylose-), green (multisugar-) and violet (sugar alcohol-binding proteins). Proteins, which do not belong to any cluster are marked in red. The protein TTHV089 in the cluster of xylose-binding proteins is shown in red box.
(B) Structural superimposition of the active site of TTHV089 (green), EcXBP (PDB ID:
3MA0, violet), galactose- (PDB ID: 3URM, blue) and glucose-binding (PDB ID: 4YS6, orange) proteins. The amino acid residues involved in the sugar binding are shown in ball- and-stick model and rest of the protein is displayed in cartoon. (C) Active site structural difference among TTHV089, xylose-, galactose- and glucose-bound proteins with respect to the position of Glu12, Leu14, Ser15 and Leu27 shown in ball-and stick-model. (D, E, F) Schematic representation of binding of EcXBP with xylose, galactose and glucose, respectively. Residues involved in interaction are shown in violet ball-and-stick model and rest of the protein in cartoon. Hydrogen bonds established between the residues and OH group of sugar are depicted with dotted lines. (G, H, I) Xylose, galactose and glucose binding to the protein TTHV089. The amino acid residues involved hydrogen bonding (dotted line) with the sugar molecule are labeled and shown in green ball-and-stick model.
The residue Glu12 (green) in TTHV089 causes the flipping of galactose and glucose (grey) in the active site with respect to galactose and glucose (yellow) of galactose- and glucose- binding proteins, respectively. (J) Genetic organization of genes associated with xylose transport and metabolism in E. coli K-12 and T. thermophilus HB8. Each gene is represented by an arrow (indicating its direction of transcription), ORF number and respective encoded proteins. The respective genes in both the bacteria are shown as ABC transporter components (green), xylose isomerase (violet), xylulose kinase (magenta), transcription regulator (blue) and α-amylase (yellow).
transporter (ORF IDs: TTC1627-TTC1629) (Silva et al., 2005), which shares a 100%
sequence identity and query coverage with the protein TTHA0356 of T. thermophilus HB8, suggesting it to be a trehalose/maltose-binding protein. However, a search for homologous proteins of TTHA0356 against the UniProtKB database produces di-, tri- and tetra- saccharide-binding proteins with the sequence identities in the range of 23-39% (query coverage: 57-89%). Further, a phylogenetic analysis of these proteins groups into three different clusters viz. di-, tri- and tetra-saccharide-binding proteins; where the protein TTHA0356 clusters with the disaccharide-binding protein (Figure 3.2A). To further affirm its cognate substrate, tertiary structure of the protein TTHA0356 was predicted; expectedly, all the programs utilized trehalose/maltose-binding protein (TMBP) from Thermococcus litoralis (PDB ID: 1EU8) as the default template. Also, it suggests the preference of disaccharides over tri- and tetra-saccharides to the protein TTHA0356. Furthermore, a comparison of the protein sequences of TTHA0356 and TMBP shows that, except Thr44 and Tyr121, all the residues Glu17, Thr46, Arg49, Asp70, Asp123, Glu239, Gly294, Trp295 and Arg364 coordinating the trehalose molecule in the active site of TMBP, are conserved in TTHA0356 as well (Figure 3.2B). Superimposition of the active site of TMBP and TTHA0356 reveals that, except the residue Glu17, all other residues holding trehalose occupy the same position and orientation (Figure 3.2C). Altogether, these results indicate that the protein TTHA0356 is a disaccharide-binding protein and can bind trehalose.
Although the protein TTHA0356 seems to bind trehalose, its closest homolog TMBPs (ORF IDs: TTC1627 and OCC03562 (PDB ID: 1EU8) from T. thermophilus HB27 and T.
litoralis, respectively) show higher binding affinity towards glucose and maltose also (Silva et al., 2005; Diez et al., 2001; Herman et al., 2006; Herman et al., 2007; Povarova et al., 2010; Fonin et al., 2014). Further, it is suggested that two loops (L1 and L2) and three helices (H1, H2 and H3) of sugar SBPs determine the substrate types which can be accommodated in the active site of the protein (Cuneo et al., 2009a). Thus, to investigate whether the protein TTHA0356 has a similar property, we compared the active-site pocket of TTHA0356 along with its structural homologs identified via Dali search (Table A.2).
An analysis of four subsites (A-D) of TTHA0356 active site indicates the occupancy of subsite C by the residue Glu174 from helix H3; and thus the availability of only two
subsites (A-B) hints the binding of either mono- (e.g. glucose) or di-saccharides (e.g.
trehalose and maltose) (Figure 3.2D). To further substantiate the hypothesis, molecular docking experiments of the protein TTHA0356 with mono- (glucose) and di-saccharide (trehalose and maltose) sugars were performed. The glucose molecule can bind the protein and occupy subsite either A or B with binding affinity of -5.66 and -6.09 kcal mol-1, respectively (Figure A.3A and Table A.3), whereas trehalose and maltose both occupy subsites A-B in the active site of the protein (Table A.3). Interestingly, maltose shows higher binding affinity (-10.22 kcal mol-1) compared to trehalose (-8.47 kcal mol-1) coordinated by a large number of hydrogen bonds (Figure A.3B and Table A.3). An earlier study using molecular dynamics simulation showed the flipping of two glucose units (Glc1 and Glc2) of trehalose into a “maltose-like” configuration of the TMBP (Herman et al., 2007). To investigate a similar process in TTHA0356, we compared the two glucose units of trehalose and maltose docked in subsites A and B. Indeed, the two glucose units prefer a “maltose-like” orientation rather than “trehalose-like” signifying the preference of maltose over trehalose to the protein TTHA0356 (Figure A.3C).
As mentioned, in thermophiles, trehalose is predominantly taken up inside the cell through trehalose/maltose ABC transporter (Silva et al., 2005). However, specific reasons for sugars like glucose, trehalose and maltose being imported by the same ABC transporter are not well known. Thus, to unriddle this enigma, we looked into the genetic mapping of trehalose/maltose ABC transporters and genes involved in trehalose synthesis. Trehalose biosynthesis pathway involves two enzymes namely trehalose-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP), encoded by genes otsA and otsB, respectively (Giaever et al., 1988). These two enzymes synthesize trehalose from glucose- 6-phosphate, which is generated during glycolysis or by interconversion of glucose-1- phosphate by the phosphoglucomutase (PGM) enzyme (Li et al., 2010). On the other hand, trehalose can also be synthesized from maltose by the enzyme trehalose synthase (TreS), encoded by the gene treS (Koh et al., 1998). Out of these, two genes otsB and treS have already been identified in T. thermophilus HB8 (Alarico et al., 2005); presence of which suggests the synthesis of trehalose by both the pathways (Figure A.4). An earlier study reported that in trehalose-deficient medium, T. thermophilus RQ-1 cells maintain the
intracellular trehalose level by importing it from extracellular environment or by synthesizing it from glucose and maltose via otsA/otsB and treS genes, respectively (Silva et al., 2003). This observation suggests that transport of glucose and maltose is essential to maintain the intracellular levels of trehalose. Furthermore, in T. thermophilus HB8, the gene pgm is located upstream to the trehalose/maltose ABC transporter genes (Figure 3.2E). In T. litoralis the enzyme trehalose glycosyl transferring synthase (TreT), which catalyzes the breakdown of trehalose, is located upstream to the trehalose/maltose ABC transporter genes (Figure 3.2E) suggesting that the bacterium uses trehalose as a carbon source and not as an osmolyte like T. thermophilus HB8, which lacks the enzyme TreT (Qu et al., 2004). Altogether, these observations demonstrate the reason for the transport of glucose and maltose along with the trehalose by trehalose/maltose ABC transporter.
Figure 3.2. Schematic representation of phylogenetic, active site and genetic organization of protein TTHA0356. (A) Phylogenetic analysis of di- (green), tri- (blue) and tetra-saccharide-binding (red) proteins along with TTHA0356. The protein sequences used for the analysis are TTHA0356, T. thermophilus HB8 (Q5SLD7); Tl_TMBP, Thermococcus litoralis (Q7LYW7); Sg_GacH, Streptomyces glaucescens (B0B0V1);
Xa_SBP, Xanthomonas axonopodis pv. Citri (Q8PK66); Af_MBP, Agrobacterium fabrum (A9CGI0); Tt_MBP, T. thermophilus HB27 (Q72I44) and Cp_MnBP, Caldanaerobius polysaccharolyticus (L0E2M2). The UniProt ID of each protein is provided in parenthesis.
(B) Pairwise sequence alignment of protein TTHA0356 and TMBP. To get a clear view, only the partial segment of the alignment has been shown here. The conserved residues and
trehalose-interacting residues across the proteins are enclosed in a red and green boxes, respectively. (C) Overlay of active-site pocket of protein TTHA0356 and TMBP. The trehalose molecule and its interacting residues of TMBP are shown as ball-and-stick model in green and yellow, respectively. The position and orientation of the conserved residues of TTHA0356 are depicted as ball-and-stick model in blue. Hydrogen bonds are represented by black-dashed lines and water molecules are shown as red spheres. (D) Schematic representation of four subsites of TTHA0356. The loop (L1) and three helices (H1, H2 and H3) anchoring the subsites are shown in blue; rest of the protein are shown in cyan. Each subsite (A-D) are partitioned by a dotted vertical line. Occupancy of mono-, di- , tri- and tetra-saccharide in four subsites is shown by overlaying TTHA0356 with structural homologs such as D-tagatose- (PDB ID: 5CI5), trehalose- (PDB ID: 1EU8), maltotriose- (PDB ID: 4QRZ and 2GH9) and maltotetraose-binding proteins (PDB ID:
3K00). (E) Genetic organization of genes involved in trehalose transport and metabolism in T. thermophilus HB8 and T. litoralis. Each gene is represented by an arrow indicating its direction of transcription, ORF number and respective encoded proteins. The ORFs are represented in different colors such as ABC transporter, blue; phosphoglucomutase (PGM), green; trehalose synthase (TreS), dark green; trehalose-6-phosphate phosphatase (TPP), purple; trehalose glycosyltransferring synthase (TreT), yellow and fructokinase, red.