8QDE image
Deposition Date 2023-08-29
Release Date 2024-09-11
Last Version Date 2025-12-17
Entry Detail
PDB ID:
8QDE
Keywords:
Title:
Crystal structure of a truncated human L-Lactate Dehydrogenase B protein in complex with NADH and oxamate
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
2.98 Å
R-Value Free:
0.31
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:L-lactate dehydrogenase B chain
Gene (Uniprot):LDHB
Chain IDs:A, B, C, D
Chain Length:330
Number of Molecules:4
Biological Source:Homo sapiens
Primary Citation
Unveiling the enzymatic activity of a dimeric LDH isoform and its implications for allosteric inhibition strategies.
Protein Sci. 34 e70367 e70367 (2025)
PMID: 41229320 DOI: 10.1002/pro.70367

Abstact

Lactate dehydrogenase (LDH) is a key enzyme in cancer metabolism, with isoforms LDH5 and LDH1 supporting glycolysis and oxidative lactate metabolism, respectively. While the development of competitive LDH inhibitors has faced diverse challenges, allosteric strategies targeting LDH tetramerization have recently attracted increasing attention. To further explore this alternative, we investigated the factors influencing LDH tetramerization and enzymatic activity using a truncated form of human LDH-B (LDHBtr), which was reported to exist predominantly as a dimer. Unexpectedly, LDHBtr exhibited measurable activity at high concentrations, correlating with increased protein stability and a structural transition to the tetrameric form. Preincubation with NADH further enhanced LDHBtr activity, stability, and self-association, consistent with cofactor-promoted tetramer assembly. Crystallographic studies confirmed the tetrameric structure of LDHBtr bound to NADH. Furthermore, reported LDH allosteric inhibitors, including cGmC9 and fluoxetine, preferentially inhibited LDHBtr compared to the native LDHB, by preventing tetramer formation. Overall, this work highlights the central role of tetramerization in regulating LDH activity, and the therapeutic potential of targeting this process. It also establishes LDHBtr as a valuable tool for screening tetramerization disruptors, paving the way for next-generation LDH inhibitors to target cancer metabolism.

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