8SG0

Crystal Structure of GDP-manose 3,5 epimerase de Myrciaria dubia in complex with substrate, product and NAD

Summary for 8SG0

• Entry DOI: 10.2210/pdb8sg0/pdb
• Descriptor: GDP-mannose 3,5-epimerase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, SULFATE ION, ... (6 entities in total)
• Functional Keywords: l-galactose 1-dehydrogenase, enzyme, plant protein
• Biological source: Myrciaria dubia
• Total number of polymer chains: 2
• Total formula weight: 96941.77

Authors

Santillan, J.A.V.,Cabrejos, D.A.L.,Pereira, H.M.,Gomez, J.C.C.,Garratt, R.C. (deposition date: 2023-04-11, release date: 2024-03-13, Last modification date: 2024-05-15)

Primary citation

Vargas, J.A.,Sculaccio, S.A.,Pinto, A.P.A.,Pereira, H.D.,Mendes, L.F.S.,Flores, J.F.,Cobos, M.,Castro, J.C.,Garratt, R.C.,Leonardo, D.A.
Structural insights into the Smirnoff-Wheeler pathway for vitamin C production in the Amazon fruit camu-camu.
J.Exp.Bot., 75:2754-2771, 2024

PubMed Abstract: l-Ascorbic acid (AsA, vitamin C) is a pivotal dietary nutrient with multifaceted importance in living organisms. In plants, the Smirnoff-Wheeler pathway is the primary route for AsA biosynthesis, and understanding the mechanistic details behind its component enzymes has implications for plant biology, nutritional science, and biotechnology. As part of an initiative to determine the structures of all six core enzymes of the pathway, the present study focuses on three of them in the model species Myrciaria dubia (camu-camu): GDP-d-mannose 3',5'-epimerase (GME), l-galactose dehydrogenase (l-GalDH), and l-galactono-1,4-lactone dehydrogenase (l-GalLDH). We provide insights into substrate and cofactor binding and the conformational changes they induce. The MdGME structure reveals a distorted substrate in the active site, pertinent to the catalytic mechanism. Mdl-GalDH shows that the way in which NAD+ association affects loop structure over the active site is not conserved when compared with its homologue in spinach. Finally, the structure of Mdl-GalLDH is described for the first time. This allows for the rationalization of previously identified residues which play important roles in the active site or in the formation of the covalent bond with FAD. In conclusion, this study enhances our understanding of AsA biosynthesis in plants, and the information provided should prove useful for biotechnological applications.

PubMed: 38224521
DOI: 10.1093/jxb/erae016

Experimental method

X-RAY DIFFRACTION (1.25 Å)