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 5ITG | pdb_00005itg

Crystal structure of D-sorbitol dehydrogenase in substrate-free form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.253 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.225 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5ITG

This is version 1.1 of the entry. See complete history. 

Literature

A highly efficient sorbitol dehydrogenase from Gluconobacter oxydans G624 and improvement of its stability through immobilization

Kim, T.S., Patel, S.K., Selvaraj, C., Jung, W.S., Pan, C.H., Kang, Y.C., Lee, J.K.

(2016) Sci Rep 6: 33438-33438

  • DOI: https://doi.org/10.1038/srep33438
  • Primary Citation Related Structures: 
    5ITG

  • PubMed Abstract: 

    A sorbitol dehydrogenase (GoSLDH) from Gluconobacter oxydans G624 (G. oxydans G624) was expressed in Escherichia coli BL21(DE3)-CodonPlus RIL. The complete 1455-bp codon-optimized gene was amplified, expressed, and thoroughly characterized for the first time. GoSLDH exhibited Km and kcat values of 38.9 mM and 3820 s(-1) toward L-sorbitol, respectively. The enzyme exhibited high preference for NADP(+) (vs. only 2.5% relative activity with NAD(+)). GoSLDH sequencing, structure analyses, and biochemical studies, suggested that it belongs to the NADP(+)-dependent polyol-specific long-chain sorbitol dehydrogenase family. GoSLDH is the first fully characterized SLDH to date, and it is distinguished from other L-sorbose-producing enzymes by its high activity and substrate specificity. Isothermal titration calorimetry showed that the protein binds more strongly to D-sorbitol than other L-sorbose-producing enzymes, and substrate docking analysis confirmed a higher turnover rate. The high oxidation potential of GoSLDH for D-sorbitol was confirmed by cyclovoltametric analysis. Further, stability of GoSLDH significantly improved (up to 13.6-fold) after cross-linking of immobilized enzyme on silica nanoparticles and retained 62.8% residual activity after 10 cycles of reuse. Therefore, immobilized GoSLDH may be useful for L-sorbose production from D-sorbitol.


  • Organizational Affiliation: 
    • Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea.

Macromolecule Content 

  • Total Structure Weight: 108.31 kDa 
  • Atom Count: 7,824 
  • Modeled Residue Count: 968 
  • Deposited Residue Count: 968 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sorbitol dehydrogenase
A, B
484Gluconobacter oxydansMutation(s): 0 
UniProt
Find proteins for Q9KWR5 (Gluconobacter oxydans)
Explore Q9KWR5 
Go to UniProtKB:  Q9KWR5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KWR5
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.253 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.225 (DCC) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.996α = 90
b = 72.996β = 90
c = 97.269γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data processing
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary