6KTL

Crystal structure of scyllo-inositol dehydrogenase R178A mutant, complexed with NAD and myo-inositol, from Paracoccus laeviglucosivorans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Single amino acid mutation altered substrate specificity for L-glucose and inositol inscyllo-inositol dehydrogenase isolated fromParacoccus laeviglucosivorans.

Suzuki, M.Koubara, K.Takenoya, M.Fukano, K.Ito, S.Sasaki, Y.Nakamura, A.Yajima, S.

(2020) Biosci Biotechnol Biochem 84: 734-742

  • DOI: https://doi.org/10.1080/09168451.2019.1702870
  • Primary Citation of Related Structures:  
    6KTJ, 6KTK, 6KTL

  • PubMed Abstract: 

    scyllo- inositol dehydrogenase, isolated from Paracoccus laeviglucosivorans (Pl-sIDH), exhibits a broad substrate specificity: it oxidizes scyllo - and myo -inositols as well as L-glucose, converting L-glucose to L-glucono-1,5-lactone. Based on the crystal structures previously reported, Arg178 residue, located at the entry port of the catalytic site, seemed to be important for accepting substrates. Here, we report the role of Arg178 by using an alanine-substituted mutant for kinetic analysis as well as to determine the crystal structures. The wild-type Pl-sIDH exhibits the activity for scyllo -inositol most preferably followed by myo -inositol and L-glucose. On the contrary, the R178A mutant abolished the activities for both inositols, but remained active for L-glucose to the same extent as its wild-type. Based on the crystal structures of the mutant, the side chain of Asp191 flipped out of the substrate binding site. Therefore, Arg178 is important in positioning Asp191 correctly to exert its catalytic activities. Abbreviations: IDH: inositol dehydrogenase; LB: Luria-Bertani; k cat : catalyst rate constant; K m : Michaelis constant; NAD: nicotinamide dinucleotide; NADH: nicotinamide dinucleotide reduced form; PDB; Protein Data Bank; PDB entry: 6KTJ, 6KTK, 6KTL.


  • Organizational Affiliation

    Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity
A, B, C, D
380Paracoccus laeviglucosivoransMutation(s): 1 
Gene Names: lgdA
UniProt
Find proteins for K7ZP76 (Paracoccus laeviglucosivorans)
Explore K7ZP76 
Go to UniProtKB:  K7ZP76
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK7ZP76
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
F [auth A],
G [auth B],
I [auth C],
K [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
INS (Subject of Investigation/LOI)
Query on INS

Download Ideal Coordinates CCD File 
L [auth D]1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
C6 H12 O6
CDAISMWEOUEBRE-GPIVLXJGSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.592α = 90
b = 128.191β = 90
c = 137.429γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan16H04895

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2020-03-04
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description