4PRK

Crystal structure of D-lactate dehydrogenase (D-LDH) from Lactobacillus jensenii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1016/j.ijbiomac.2014.04.048
  • Primary Citation of Related Structures:  

  • 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 bi ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-phosphoerythronate dehydrogenase
A, B
336N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.532α = 90.00
b = 90.532β = 90.00
c = 157.780γ = 120.00
Software Package:
Software NamePurpose
RESOLVEphasing
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
SOLVEphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-03-06 
  • Released Date: 2014-06-18 
  • Deposition Author(s): Kim, S., Kim, K.J.

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release