2YQ5 | pdb_00002yq5

Crystal Structure of D-isomer specific 2-hydroxyacid dehydrogenase from Lactobacillus delbrueckii ssp. bulgaricus: NAD complexed form

• PDB DOI: https://doi.org/10.2210/pdb2YQ5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Lactobacillus delbrueckii subsp. bulgaricus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-05 Released: 2012-11-21 
• Deposition Author(s): Holton, S.J., Anandhakrishnan, M., Geerlof, A., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structural Characterization of D-Isomer Specific 2-Hydroxyacid Dehydrogenase from Lactobacillus Delbrueckii Ssp. Bulgaricus

Holton, S.J., Anandhakrishnan, M., Geerlof, A., Wilmanns, M.

(2013) J Struct Biol 181: 179

• PubMed: 23110853 
• DOI: https://doi.org/10.1016/j.jsb.2012.10.009
• Primary Citation of Related Structures:  
  2YQ4, 2YQ5


• PubMed Abstract: 
  

  Hydroxyacid dehydrogenases, responsible for the stereospecific conversion of 2-keto acids to 2-hydroxyacids in lactic acid producing bacteria, have a range of biotechnology applications including antibiotic synthesis, flavor development in dairy products and the production of valuable synthons. The genome of Lactobacillus delbrueckii ssp. bulgaricus, a member of the heterogeneous group of lactic acid bacteria, encodes multiple hydroxyacid dehydrogenases whose structural and functional properties remain poorly characterized. Here, we report the apo and coenzyme NAD⁺ complexed crystal structures of the L. bulgaricusD-isomer specific 2-hydroxyacid dehydrogenase, D2-HDH. Comparison with closely related members of the NAD-dependent dehydrogenase family reveals that whilst the D2-HDH core fold is structurally conserved, the substrate-binding site has a number of non-canonical features that may influence substrate selection and thus dictate the physiological function of the enzyme.

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Organizational Affiliation: 

EMBL c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 154.77 kDa 
• Atom Count: 10,369 
• Modelled Residue Count: 1,308 
• Deposited Residue Count: 1,372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE	A, B, C, D	343	Lactobacillus delbrueckii subsp. bulgaricus	Mutation(s): 0
UniProt
Find proteins for Q1GAA2 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14)) Explore Q1GAA2  Go to UniProtKB:  Q1GAA2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.718	α = 90
b = 110.012	β = 90
c = 147.736	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-21 
Deposition Author(s): Holton, S.J., Anandhakrishnan, M., Geerlof, A., Wilmanns, M.

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 1.1: 2013-02-20
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description