PDBsum entry: 1m53

Isomerase

PDB id: 1m53

Contents

Protein chain

556 a.a. *

Waters ×303

* Residue conservation analysis

PDB id:

1m53

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.

Resolution:

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

Date:

08-Jul-02 Release date: 08-Jul-03

Protein chain

Q8KR84  (Q8KR84_9ENTR) -  Isomaltulose synthase

Seq: 598 a.a.

Struc: 556 a.a.

 Gene Ontology (GO) functional annotation 

• 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.

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 2.5 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.