8HPE

Crystal structure of Leucine dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

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Ligand Structure Quality Assessment 


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Literature

A Tri-Enzyme Cascade for Efficient Production of L-2-Aminobutyrate from L-Threonine.

Li, X.Gao, C.Wei, W.Song, W.Meng, W.Liu, J.Chen, X.Gao, C.Guo, L.Liu, L.Wu, J.

(2023) Chembiochem 24: e202300148-e202300148

  • DOI: https://doi.org/10.1002/cbic.202300148
  • Primary Citation of Related Structures:  
    8HPE, 8HR6

  • PubMed Abstract: 

    L-2-aminobutyrate (L-ABA) is an important chiral drug intermediate with a key role in modern medicinal chemistry. Here, we describe the development of an efficient method for the asymmetric synthesis of L-ABA in a tri-enzymatic cascade in Escherichia coli BL21 (DE3) using a cost-effective L-Thr. Low activity of leucine dehydrogenase from Bacillus thuringiensis (BtLDH) and unbalanced expression of enzymes in the cascade were major challenges. Mechanism-based protein engineering generated the optimal triple variant BtLDH M3 (A262S/V296C/P150M) with 20.7-fold increased specific activity and 9.6-fold increased k cat /K m compared with the wild type. Optimizing plasmids with different copy numbers regulated enzymatic expression, thereby increasing the activity ratio (0.3 : 1:0.6) of these enzymes in vivo close to the optimal ratio (0.4 : 1 : 1) in vitro. Importing the optimal triple mutant BtLDH M3 into our constructed pathway in vivo and optimization of transformation conditions achieved one-pot conversion of L-Thr to 130.2 g/L L-ABA, with 95 % conversion, 99 % e.e. and 10.9 g L -1  h -1 productivity (the highest to date) in 12 h on a 500 mL scale. These results describe a potential biosynthesis approach for the industrial production of L-ABA.


  • Organizational Affiliation

    School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine dehydrogenase
A, B
366Bacillus thuringiensisMutation(s): 0 
Gene Names: ldh1BK774_17255BK775_32270BTGOE4_46100BUM91_06765C5676_00473D7J84_18335GH851_02505GH891_02550
EC: 1.4.1.9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
P [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
M [auth A],
Q [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.949α = 90
b = 120.949β = 90
c = 177.624γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release