PDBsum entry 1m53

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Isomerase PDB id
Protein chain
556 a.a. *
Waters ×303
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of isomaltulose synthase (pali) from klebsiella sp. Lx3
Structure: Isomaltulose synthase. Chain: a. Fragment: residues 29-598. Engineered: yes
Source: Klebsiella sp. Lx3. Organism_taxid: 167956. Gene: pali. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.20Å     R-factor:   0.194     R-free:   0.242
Authors: N.Li,K.Swaminathan
Key ref:
D.Zhang et al. (2003). Isomaltulose synthase (PalI) of Klebsiella sp. LX3. Crystal structure and implication of mechanism. J Biol Chem, 278, 35428-35434. PubMed id: 12819210 DOI: 10.1074/jbc.M302616200
08-Jul-02     Release date:   08-Jul-03    
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Protein chain
Pfam   ArchSchema ?
Q8KR84  (Q8KR84_9ENTR) -  Isomaltulose synthase
598 a.a.
556 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     2 terms  


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.
Isomaltulose synthase from Klebsiella sp. LX3 (PalI, EC 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 2.5 level. 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: 572, and PalI: 545 are indicated by the symbol x. For clarity, only the residues that form important salt bridges and hydrogen bonds that are disrupted by the truncations are shown.
  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
21229265 B.Ren, S.Li, H.Xu, X.H.Feng, H.Cai, and Q.Ye (2011).
Purification and characterization of a highly selective sucrose isomerase from Erwinia rhapontici NX-5.
  Bioprocess Biosyst Eng, 34, 629-637.  
20492546 D.Hamerli, and R.G.Birch (2011).
Transgenic expression of trehalulose synthase results in high concentrations of the sucrose isomer trehalulose in mature stems of field-grown sugarcane.
  Plant Biotechnol J, 9, 32-37.  
20589449 S.Li, H.Cai, Y.Qing, B.Ren, H.Xu, H.Zhu, and J.Yao (2011).
Cloning and characterization of a sucrose isomerase from Erwinia rhapontici NX-5 for isomaltulose hyperproduction.
  Appl Biochem Biotechnol, 163, 52-63.  
20517292 J.Chillarón, M.Font-Llitjós, J.Fort, A.Zorzano, D.S.Goldfarb, V.Nunes, and M.Palacín (2010).
Pathophysiology and treatment of cystinuria.
  Nat Rev Nephrol, 6, 424-434.  
19966417 E.Champion, M.Remaud-Simeon, L.K.Skov, J.S.Kastrup, M.Gajhede, and O.Mirza (2009).
The apo structure of sucrose hydrolase from Xanthomonas campestris pv. campestris shows an open active-site groove.
  Acta Crystallogr D Biol Crystallogr, 65, 1309-1314.
PDB code: 2wpg
19783746 H.Watzlawick, and R.Mattes (2009).
Gene cloning, protein characterization, and alteration of product selectivity for the trehalulose hydrolase and trehalulose synthase from "Pseudomonas mesoacidophila" MX-45.
  Appl Environ Microbiol, 75, 7026-7036.  
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.  
18398906 T.Shirai, V.S.Hung, K.Morinaka, T.Kobayashi, and S.Ito (2008).
Crystal structure of GH13 alpha-glucosidase GSJ from one of the deepest sea bacteria.
  Proteins, 73, 126-133.
PDB code: 2ze0
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
  16508103 S.Ravaud, H.Watzlawick, R.Haser, R.Mattes, and N.Aghajari (2005).
Expression, purification, crystallization and preliminary X-ray crystallographic studies of the trehalulose synthase MutB from Pseudomonas mesoacidophila MX-45.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 100-103.
PDB code: 1zjb
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.