Crystal Structure of the Lactate Dehydrogenase of Cyanobacterium Aponinum in its apo form.

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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Deciphering Evolutionary Trajectories of Lactate Dehydrogenases Provides New Insights into Allostery.

Robin, A.Y.Brochier-Armanet, C.Bertrand, Q.Barette, C.Girard, E.Madern, D.

(2023) Mol Biol Evol 40

  • DOI: https://doi.org/10.1093/molbev/msad223
  • Primary Citation of Related Structures:  
    8AB2, 8AB3

  • PubMed Abstract: 

    Lactate dehydrogenase (LDH, EC.1.1.127) is an important enzyme engaged in the anaerobic metabolism of cells, catalyzing the conversion of pyruvate to lactate and NADH to NAD+. LDH is a relevant enzyme to investigate structure-function relationships. The present work provides the missing link in our understanding of the evolution of LDHs. This allows to explain (i) the various evolutionary origins of LDHs in eukaryotic cells and their further diversification and (ii) subtle phenotypic modifications with respect to their regulation capacity. We identified a group of cyanobacterial LDHs displaying eukaryotic-like LDH sequence features. The biochemical and structural characterization of Cyanobacterium aponinum LDH, taken as representative, unexpectedly revealed that it displays homotropic and heterotropic activation, typical of an allosteric enzyme, whereas it harbors a long N-terminal extension, a structural feature considered responsible for the lack of allosteric capacity in eukaryotic LDHs. Its crystallographic structure was solved in 2 different configurations typical of the R-active and T-inactive states encountered in allosteric LDHs. Structural comparisons coupled with our evolutionary analyses helped to identify 2 amino acid positions that could have had a major role in the attenuation and extinction of the allosteric activation in eukaryotic LDHs rather than the presence of the N-terminal extension. We tested this hypothesis by site-directed mutagenesis. The resulting C. aponinum LDH mutants displayed reduced allosteric capacity mimicking those encountered in plants and human LDHs. This study provides a new evolutionary scenario of LDHs that unifies descriptions of regulatory properties with structural and mutational patterns of these important enzymes.

  • Organizational Affiliation

    Université Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-lactate dehydrogenase337Cyanobacterium aponinumMutation(s): 0 
Gene Names: ldhCyan10605_1816
Find proteins for K9Z684 (Cyanobacterium aponinum (strain PCC 10605))
Explore K9Z684 
Go to UniProtKB:  K9Z684
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9Z684
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.797α = 90
b = 103.797β = 90
c = 197.824γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
MxCuBEdata collection
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other governmentFranceprogram CrysFrag R&D booster region AuRA
Other governmentFranceProgram XO4_2.0 Pack ambition recherche region AuRA

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Database references