9CP9

Crystal structure of DHPS-3-dehydrogenase, HpsN H319A variant from Cupriavidus pinatubonensis in complex with substrate (R-DHPS) and NADH

This is a non-PDB format compatible entry.

Summary for 9CP9

• Entry DOI: 10.2210/pdb9cp9/pdb
• Related: 8V35 8V36 8V37
• Descriptor: Sulfopropanediol 3-dehydrogenase, ZINC ION, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, ... (6 entities in total)
• Functional Keywords: dhps-3-dehydrogenase, oxidoreductase
• Biological source: Cupriavidus pinatubonensis JMP134
• Total number of polymer chains: 2
• Total formula weight: 95910.42

Authors

Lee, M. (deposition date: 2024-07-18, release date: 2024-09-25, Last modification date: 2024-10-09)

Primary citation

Burchill, L.,Kaur, A.,Nastasovici, A.,Lee, M.,Williams, S.J.
Structural and kinetic insights into the stereospecific oxidation of R -2,3-dihydroxypropanesulfonate by DHPS-3-dehydrogenase from Cupriavidus pinatubonensis.
Chem Sci, 15:15757-15768, 2024

PubMed Abstract: 2,3-Dihydroxypropanesulfonate (DHPS) and sulfolactate (SL) are environmentally important organosulfur compounds that play key roles as metabolic currencies in the sulfur cycle. Despite their prevalence, the pathways governing DHPS and SL production remain poorly understood. Here, we study DHPS-3-dehydrogenase from (HpsN), a bacterium capable of utilizing DHPS as a sole carbon source. Kinetic analysis of HpsN reveals a strict preference for -DHPS, catalyzing its 4-electron oxidation to -SL, with high specificity for NAD over NADP. The 3D structure of HpsN in complex with Zn, NADH and -SL, elucidated through X-ray crystallography, reveals a fold akin to bacterial and plant histidinol dehydrogenases with similar coordination geometry around the octahedral Zn centre and involving the sulfonate group as a ligand. A key residue, His126, distinguishes DHPS dehydrogenases from histidinol dehydrogenases, by structural recognition of the sulfonate substrate of the former. Site-directed mutagenesis pinpoints Glu318, His319, and Asp352 as active-site residues important for the catalytic activity of HpsN. Taxonomic and pathway distribution analysis reveals the prevalence of HpsN homologues within different pathways of DHPS catabolism and across bacterial classes including Alpha-, Beta-, Gamma-, and Deltaproteobacteria and Desulfobacteria, emphasizing its importance in the biogeochemical sulfur cycle.

PubMed: 39263660
DOI: 10.1039/d4sc05114a

Experimental method

X-RAY DIFFRACTION (2.013 Å)