9EID

A broad-substrate spectrum lactate racemase A from Isosphaera pallida in complex with D-2-Hydroxybutyrate

Summary for 9EID

• Entry DOI: 10.2210/pdb9eid/pdb
• Descriptor: A broad-substrate spectrum lactate racemase A, (2R)-2-oxidanylbutanoic acid, 3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium, ... (6 entities in total)
• Functional Keywords: catalytic activity, isomerase activity, racemase and epimerase activity racemase acting on hydroxy acids and derivatives, isomerase
• Biological source: Isosphaera pallida
• Total number of polymer chains: 1
• Total formula weight: 46605.82

Authors

Gatreddi, S.,Hausinger, R.P.,Hu, J. (deposition date: 2024-11-25, release date: 2025-01-29)

Primary citation

Gatreddi, S.,Urdiain-Arraiza, J.,Desguin, B.,Hausinger, R.P.,Hu, J.
Structural Basis for Catalysis and Substrate Specificity of a LarA Racemase with a Broad Substrate Spectrum.
Biorxiv, 2024

PubMed Abstract: The LarA family consists of diverse racemases/epimerases that interconvert the diastereomers of a variety of α-hydroxyacids by using a nickel-pincer nucleotide (NPN) cofactor. The hidden redox reaction catalyzed by the NPN cofactor makes LarA enzymes attractive engineering targets for applications. However, how a LarA enzyme binds its natural substrate and recognizes different α-hydroxyacids has not been elucidated. Here, we report three high-resolution structures of the enzyme-substrate complexes of a broad-spectrum LarA enzyme from (LarA ). The substrate binding mode reveals an optimal orientation and distance between the hydride donor and acceptor, strongly supporting the proposed proton-coupled hydride transfer mechanism. The experimentally solved structures, together with the structural models of other LarA enzymes, allow us to identify the residues/structural elements critically involved in the interactions with different α-hydroxyacid substrates. Collectively, this work provides a critical structural basis for catalysis and substrate recognition of the diverse enzymes in the LarA family, thus building a foundation for enzyme engineering.

PubMed: 39651260
DOI: 10.1101/2024.11.28.625916

Experimental method

X-RAY DIFFRACTION (1.38 Å)