Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 75.53 kDa 
• Atom Count: 5209 
• Modelled Residue Count: 660 
• Deposited Residue Count: 672 
• Unique protein chains: 1

4PRL

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

• PDB DOI: 10.2210/pdb4PRL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Lactobacillus jensenii 1153
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.278 
• R-Value Work: 0.211 
• R-Value Observed: 0.228 

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

• PubMed: 24794195 
• DOI: 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.

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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. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-phosphoerythronate dehydrogenase	A, B	336	Lactobacillus jensenii 1153	Mutation(s): 0  Gene Names: pdxB, LBJG_01197 EC: 1.1.1.290

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 90.714	α = 90
b = 90.714	β = 90
c = 158.183	γ = 120

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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