1LTH

T AND R STATES IN THE CRYSTALS OF BACTERIAL L-LACTATE DEHYDROGENASE REVEAL THE MECHANISM FOR ALLOSTERIC CONTROL

• PDB DOI: https://doi.org/10.2210/pdb1LTH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bifidobacterium longum subsp. longum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1995-01-04 Released: 1995-03-31 
• Deposition Author(s): Iwata, S., Ohta, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.188 
• R-Value Observed: 0.188 

Literature

T and R states in the crystals of bacterial L-lactate dehydrogenase reveal the mechanism for allosteric control.

Iwata, S., Kamata, K., Yoshida, S., Minowa, T., Ohta, T.

(1994) Nat Struct Biol 1: 176-185

• PubMed: 7656036 
• DOI: https://doi.org/10.1038/nsb0394-176
• Primary Citation of Related Structures:  
  1LTH


• PubMed Abstract: 
  

  The crystal structure of L-lactate dehydrogenase from Bifidobacterium longum, determined to 2.5 A resolution, contains a regular 1:1 complex of T- and R-state tetramers. A comparison of these two structures within the same crystal lattice and kinetical characterization of the T-R transition in solution provide an explanation for the molecular mechanism of allosteric activation. Substrate affinity is controlled by helix sliding between subunits which is triggered by the binding of the activator, fructose 1,6-bisphosphate. The proposed mechanism can explain activation by chemical modification and mutagenesis, as well as suggesting why vertebrate counterparts are not allosteric.

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Organizational Affiliation: 

Department of Agricultural Chemistry, University of Tokyo, 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)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 70.35 kDa 
• Atom Count: 5,135 
• 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 (T- AND R- STATE TETRAMER COMPLEX)	A [auth T], B [auth R]	319	Bifidobacterium longum subsp. longum	Mutation(s): 0  Gene Names: BIFIDOBACTERIUM LONGUM LDH GENE 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	D [auth T], F [auth R]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
FBP	C [auth T], E [auth R]	1,6-di-O-phosphono-beta-D-fructofuranose C6 H14 O12 P2 RNBGYGVWRKECFJ-ARQDHWQXSA-N
OXM	G [auth R]	OXAMIC ACID C2 H3 N O3 SOWBFZRMHSNYGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.188 
• R-Value Observed: 0.188 
• Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.4	α = 90
b = 295.9	β = 90
c = 71	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-03-31 
Deposition Author(s): Iwata, S., Ohta, T.

Revision History  

• Version 1.0: 1995-03-31
  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: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Structure summary