Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 67.25 kDa 
• Atom Count: 4951 
• Modelled Residue Count: 556 
• Deposited Residue Count: 570 
• Unique protein chains: 1

1M53

CRYSTAL STRUCTURE OF ISOMALTULOSE SYNTHASE (PALI) FROM KLEBSIELLA SP. LX3

• PDB DOI: 10.2210/pdb1M53/pdb

• Classification: ISOMERASE
• Organism(s): Klebsiella sp. LX3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-07-08 Released: 2003-07-08 
• Deposition Author(s): Li, N., Swaminathan, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.242 
• R-Value Work: 0.194 
• R-Value Observed: 0.194 

Literature

Isomaltulose synthase (PalI) of Klebsiella sp. LX3. Crystal structure and implication of mechanism

Zhang, D., Li, N., Lok, S.M., Zhang, L.-H., Swaminathan, K.

(2003) J Biol Chem 278: 35428-35434

• PubMed: 12819210 
• DOI: 10.1074/jbc.M302616200
• Primary Citation of Related Structures:  
  1M53


• PubMed 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.

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Related Citations: 

• Isomaltulose Synthase from Klebsiella sp. Strain LX3: Gene Cloning and Characterization and Engineering of Thermostability
  Zhang, D.-H., Li, X.-Z., Zhang, L.-H.
  (2002) Appl Environ Microbiol 68: 2676

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Organizational Affiliation: 

Department of Pathology, National University of Singapore, 5 Lower Kent Ridge Road, Singapore 119074.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isomaltulose Synthase	A	570	Klebsiella sp. LX3	Mutation(s): 0  Gene Names: PalI EC: 5.4.99.11
UniProt
Find proteins for Q8KR84 (Klebsiella sp. LX3) Explore Q8KR84  Go to UniProtKB:  Q8KR84

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.242 
• R-Value Work: 0.194 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.239	α = 90
b = 94.153	β = 90
c = 111.294	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-07-08 
• Released Date: 2003-07-08 
Deposition Author(s): Li, N., Swaminathan, K.

Revision History  

• Version 1.0: 2003-07-08
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance