5GWR | pdb_00005gwr

4-hydroxyisoleucine dehydrogenase complexed with NADH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.205 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Engineering a short-chain dehydrogenase/reductase for the stereoselective production of (2S,3R,4S)-4-hydroxyisoleucine with three asymmetric centers

Shi, X.Miyakawa, T.Nakamura, A.Hou, F.Hibi, M.Ogawa, J.Kwon, Y.Tanokura, M.

(2017) Sci Rep 7: 13703-13703

  • DOI: https://doi.org/10.1038/s41598-017-13978-w
  • Primary Citation Related Structures: 
    5GWR, 5GWS, 5GWT

  • PubMed Abstract: 

    Fenugreek is a dietary supplement for anti-aging and human health. (2S,3R,4S)-4-hydroxyisoleucine (4-HIL), which is extracted from fenugreek seeds, is expected to be a promising orally active drug for diabetes and diabetic nephropathy because of its insulinotropic effect. Although several chemical synthesis methods of 4-HIL have been proposed, these methods require multistep reactions to control the stereochemistry of 4-HIL. In this study, we modified the key enzyme 4-HIL dehydrogenase (HILDH) to overcome the biggest limitation in commercial-scale production of 4-HIL. As a result, an effective one-step carbonyl reduction to produce (2S,3R,4S)-4-HIL was successfully accomplished with strict stereoselectivity (>99% de). Mass production of (2S,3R,4S)-4-HIL by our synthetic method could have a significant contribution to the prevention of diabetes, dyslipidemia, and Alzheimer's disease. (120 words/200 words).


  • Organizational Affiliation
    • Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.

Macromolecule Content 

  • Total Structure Weight: 128.26 kDa 
  • Atom Count: 7,498 
  • Modeled Residue Count: 924 
  • Deposited Residue Count: 1,128 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
4-hydroxyisolecuine dehydrogenase
A, B, C, D
282Bacillus thuringiensisMutation(s): 0 
Gene Names: AC241_05390

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.205 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 231.474α = 90
b = 231.474β = 90
c = 78.675γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description