8I5Z

LDH Mutant P101Q-(An unexpected single-point mutation triggers the unleashing of catalytic potential of a NADH-dependent dehydrogenase)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Characterization of the Pro101Gln mutation that enhances the catalytic performance of T. indicus NADH-dependent d-lactate dehydrogenase.

Liu, J.Liu, G.Han, X.Tao, F.Xu, P.

(2023) Structure 31: 1616-1628.e3

  • DOI: https://doi.org/10.1016/j.str.2023.08.019
  • Primary Citation of Related Structures:  
    8I5Z

  • PubMed Abstract: 

    NADH-dependent d-lactate dehydrogenases (d-LDH) are important for the industrial production of d-lactic acid. Here, we identify and characterize an improved d-lactate dehydrogenase mutant (d-LDH1) that contains the Pro101Gln mutation. The specific enzyme activities of d-LDH1 toward pyruvate and NADH are 21.8- and 11.0-fold greater compared to the wild-type enzyme. We determined the crystal structure of Apo-d-LDH1 at 2.65 Å resolution. Based on our structural analysis and docking studies, we explain the differences in activity with an altered binding conformation of NADH in d-LDH1. The role of the conserved residue Pro101 in d-LDH was further probed in site-directed mutagenesis experiments. We introduced d-LDH1 into Bacillus licheniformis yielding a d-lactic acid production of 145.9 g L -1 within 60 h at 50°C, which was three times higher than that of the wild-type enzyme. The discovery of d-LDH1 will pave the way for the efficient production of d-lactic acid by thermophilic bacteria.


  • Organizational Affiliation

    State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein
A, B, C, D
339Thermodesulfatator indicus DSM 15286Mutation(s): 1 
Gene Names: Thein_0264
UniProt
Find proteins for F8A9V0 (Thermodesulfatator indicus (strain DSM 15286 / JCM 11887 / CIR29812))
Explore F8A9V0 
Go to UniProtKB:  F8A9V0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8A9V0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.245 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.302α = 90
b = 92.302β = 90
c = 380.013γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2023-09-06 
  • Deposition Author(s): Liu, J.Q.

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China22138007
National Science Foundation (NSF, China)China32170105

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-06
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Author supporting evidence, Refinement description, Source and taxonomy, Structure summary
  • Version 1.2: 2024-03-20
    Changes: Database references