1LLD | pdb_00001lld

MOLECULAR BASIS OF ALLOSTERIC ACTIVATION OF BACTERIAL L-LACTATE DEHYDROGENASE

• PDB DOI: https://doi.org/10.2210/pdb1LLD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bifidobacterium longum subsp. longum
• Mutation(s): No 


• Deposited: 1992-06-08 Released: 1994-01-31 
• Deposition Author(s): Iwata, S., Ohta, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 
  0.170 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Molecular basis of allosteric activation of bacterial L-lactate dehydrogenase.

Iwata, S., Ohta, T.

(1993) J Mol Biology 230: 21-27

• PubMed: 8450537 
• DOI: https://doi.org/10.1006/jmbi.1993.1122
• Primary Citation of Related Structures:  
  1LLD


• PubMed Abstract: 
  

  The three-dimensional structure of allosteric L-lactate dehydrogenase from Bifidobacterium longum, the first example of a T-state structure of L-lactate dehydrogenase, has been determined to 2.0 A. A comparative study of this structure with the previously reported R-state structure from Bacillus stearothermophilus has revealed the allosteric activation mechanism of the bacterial L-lactate dehydrogenase. The fructose 1,6-bisphosphate-induced conformational change at the effector site and the substrate affinity change at the activity site are clearly shown at a molecular level. Coupling of these changes can be simply explained by a set of concerted rotations between subunits in the tetramer of the enzyme. This T to R transition is the first example for a tetrameric allosteric protein where the rotations occur around each of three axes of symmetry.

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Organizational Affiliation: 

Photon Factory, National Laboratory for High Energy Physics, Ibaraki-ken, Japan.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 69.58 kDa 
• Atom Count: 5,010 
• Modelled Residue Count: 626 
• Deposited Residue Count: 638 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-LACTATE DEHYDROGENASE	A, B	319	Bifidobacterium longum subsp. longum	Mutation(s): 0  EC: 1.1.1.27
UniProt
Find proteins for E8ME30 (Bifidobacterium longum subsp. longum (strain ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b)) Explore E8ME30  Go to UniProtKB:  E8ME30

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: 2.00 Å
• R-Value Work:  0.170 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.8	α = 90
b = 131.4	β = 90
c = 63.8	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Iwata, S., Ohta, T.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations