Crystal structure of D-lactate dehydrogenase with NAD+ from Lactobacillus jensenii

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.228 

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Crystal structure and thermodynamic properties of d-lactate dehydrogenase from Lactobacillus jensenii.

Kim, S.Gu, S.A.Kim, Y.H.Kim, K.J.

(2014) Int J Biol Macromol 68C: 151-157

  • DOI: https://doi.org/10.1016/j.ijbiomac.2014.04.048
  • Primary Citation of Related Structures:  
    4PRK, 4PRL

  • PubMed Abstract: 

    The thermostable d-lactate dehydrogenase from Lactobacillus jensenii (Ljd-LDH) is a key enzyme in the production of the d-form of lactic acid from pyruvate concomitant with the oxidation of NADH to NAD(+). The polymers of d-lactic acid are used as biodegradable bioplastics. The crystal structures of Ljd-LDH and in complex with NAD(+) were determined at 2.13 and 2.60Å resolutions, respectively. The Ljd-LDH monomer consists of the N-terminal substrate-binding domain and the C-terminal NAD-binding domain. The Ljd-LDH forms a homodimeric structure, and the C-terminal NAD-binding domain mostly enables the dimerization of the enzyme. The NAD cofactor is bound to the GxGxxG NAD-binding motif located between the two domains. Structural comparisons of Ljd-LDH with other d-LDHs reveal that Ljd-LDH has unique amino acid residues at the linker region, which indicates that the open-close dynamics of Ljd-LDH might be different from that of other d-LDHs. Moreover, thermostability experiments showed that the T50(10) value of Ljd-LDH (54.5°C) was much higher than the commercially available d-lactate dehydrogenase (42.7°C). In addition, Ljd-LDH has at least a 7°C higher denaturation temperature compared to commercially available d-LDHs.

  • Organizational Affiliation

    School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program), Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea; School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-phosphoerythronate dehydrogenase
A, B
336Lactobacillus jensenii 1153Mutation(s): 0 
Gene Names: pdxBLBJG_01197
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C21 H27 N7 O14 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.228 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.714α = 90
b = 90.714β = 90
c = 158.183γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description