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556 a.a.
Key reference
DOI no: 10.1074/jbc.M302616200 J Biol Chem 278:35428-35434 (2003) PubMed id: 12819210
Isomaltulose synthase (PalI) of Klebsiella sp. LX3. Crystal structure and implication of mechanism. D.Zhang, N.Li, S.M.Lok, L.H.Zhang, K.Swaminathan. ABSTRACT
Isomaltulose synthase from Klebsiella sp. LX3 (PalI, EC 5.4.99.11) catalyzes the isomerization of sucrose to produce isomaltulose (alpha-D-glucosylpyranosyl-1,6-D-fructofuranose) and trehalulose (alpha-D-glucosylpyranosyl-1,1-d-fructofuranose). The PalI structure, solved at 2.2-A resolution with an R-factor of 19.4% and Rfree of 24.2%, consists of three domains: an N-terminal catalytic (beta/alpha)8 domain, a subdomain between N beta 3 and N alpha 3, and a C-terminal domain having seven beta-strands. The active site architecture of PalI is identical to that of other glycoside hydrolase family 13 members, suggesting a similar mechanism in substrate binding and hydrolysis. However, a unique RLDRD motif in the proximity of the active site has been identified and shown biochemically to be responsible for sucrose isomerization. A two-step reaction mechanism for hydrolysis and isomerization, which occurs in the same pocket is proposed based on both the structural and biochemical data. Selected C-terminal truncations have been shown to reduce and even abolish the enzyme activity, consistent with the predicted role of the C-terminal residues in the maintenance of enzyme conformation and active site topology.
Selected figure(s)
Figure 1.
FIG. 1. Structures of PalI, oligo-1,6-glucosidase, and amylosucrase. All molecules are shown in the same orientation. A, structure of PalI. The N-terminal catalytic (/
)[8] barrel is drawn in blue, the sub-domain in magenta, and the C-terminal domain in red. The isomerization region (residues 321-340) in PalI (and the equivalent regions in oligo-1,6-glucosidase and amylosucrase) are drawn in yellow. B, structure of oligo-1,6-glucosidase (10). C, structure of amylosucrase (11). Its extra N-terminal portion is shown in green.
Figure 2.
FIG. 2. Catalytic pocket, isomerization region, and N-C termini interactions in PalI. A, the 2F[o] - F[c] electron density map at the catalytic pocket is drawn at the 2.5level. The five conserved residues that participate in substrate binding and hydrolysis are labeled in green, and the five residues that are involved in the isomerization of sucrose are labeled in red. B, the superimposition of PalI on the amylosucrase-sucrose complex based on the atoms of the five conserved hydrolysis residues. PalI is blue, amylosucrase is gray, and sucrose is magenta. The residues in amylosucrase that interact with sucrose and their corresponding residues in PalI are shown. Note the deviation of the helix from the substrate in amylosucrase and the approach of the substrate by the RLDRD motif residues in PalI. Arg333 of PalI occupies the position of Arg446 in amylosucrase. C, the N- and C-terminal interactions. Hydrogen bonds are represented by dashed lines. The truncation positions of the mutants PalI:
587, PalI:
The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 35428-35434) copyright 2003.
Literature references that cite this PDB file's key reference
PubMed id Reference
19486422 J.Cha, J.H.Jung, S.E.Park, M.H.Cho, D.H.Seo, S.J.Ha, J.W.Yoon, O.H.Lee, Y.C.Kim, and C.S.Park (2009).
Molecular cloning and functional characterization of a sucrose isomerase (isomaltulose synthase) gene from Enterobacter sp. FMB-1.J Appl Microbiol, 107, 1119-1130.
18552181 H.C.Lee, J.H.Kim, S.Y.Kim, and J.K.Lee (2008).
Isomaltose production by modification of the fructose-binding site on the basis of the predicted structure of sucrose isomerase from "Protaminobacter rubrum".Appl Environ Microbiol, 74, 5183-5194.
15746363 L.Wu, and R.G.Birch (2005).
Characterization of the highly efficient sucrose isomerase from Pantoea dispersa UQ68J and cloning of the sucrose isomerase gene.Appl Environ Microbiol, 71, 1581-1590.
15659099 M.Verhaest, W.V.Ende, K.L.Roy, C.J.De Ranter, A.V.Laere, and A.Rabijns (2005).
X-ray diffraction structure of a plant glycosyl hydrolase family 32 protein: fructan 1-exohydrolase IIa of Cichorium intybus.Plant J, 41, 400-411.
PDB code: 1st8 The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.
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