8P6S

Arabidopsis thaliana DGD2 in complex with UDP-galactose

Summary for 8P6S

• Entry DOI: 10.2210/pdb8p6s/pdb
• Descriptor: Digalactosyldiacylglycerol synthase 2, chloroplastic, GALACTOSE-URIDINE-5'-DIPHOSPHATE (3 entities in total)
• Functional Keywords: glycosyltransferase, substrate, transferase
• Biological source: Arabidopsis thaliana (thale cress)
• Total number of polymer chains: 1
• Total formula weight: 48226.51

Authors

Scaletti, E.R.,Martinez-Carranza, M.,Stenmark, P. (deposition date: 2023-05-29, release date: 2024-12-11, Last modification date: 2025-06-25)

Primary citation

Scaletti Hutchinson, E.,Martinez-Carranza, M.,Fu, B.,Maler, L.,Stenmark, P.
Structure and membrane interactions of Arabidopsis thaliana DGD2, a glycosyltransferase in the chloroplast membrane.
J.Biol.Chem., 301:108431-108431, 2025

PubMed Abstract: Galactolipids are characteristic lipids of the photosynthesis membranes of higher plants and cyanobacteria. Due to their close relationship to the stability of the photosystem protein complexes, the biogenesis of galactolipids has been intensively studied on the genetic and molecular levels. There are two major types of galactolipids in chloroplastic membranes: monogalactosyldiacylglycerol and digalactosyldiacylglycerol (DGDG). Under phosphate-limiting conditions, the amount of DGDG increases dramatically to allow for phosphate salvage from phospholipids. In Arabidopsis thaliana, the membrane-associated glycosyltransferase digalactosyldiacylglycerol synthase 2 (atDGD2) is highly responsive to phosphate starvation and is significantly upregulated during such conditions. The lipid galactosylation reactions are also fundamentally interesting as they require a catalyst that is capable of bringing a hydrophilic and lipophilic substrate together at the solution-membrane phase border. Here, we present the X-ray crystal structure of atDGD2, which is the first reported DGDG synthase structure. AtDGD2 is most structurally similar to functionally unrelated GT-B enzymes. Interestingly, in spite of significant donor substrate binding differences, we identified four amino acids (Gly22, His151, Lys243, and Glu321, atDGD2 numbering) which were entirely conserved between the structurally similar enzymes. We also investigated the membrane interaction kinetics and membrane anchoring mechanism of atDGD2. This demonstrated that atDGD2 is membrane-bound but also showed that membrane binding is highly dynamic. Furthermore, our structural information in context of previous biophysical studies highlights regions of the enzyme exhibiting a high degree of structural plasticity, which we propose to be important for allowing atDGD2 to quickly adapt its activity based on the membrane lipid environment.

PubMed: 40120685
DOI: 10.1016/j.jbc.2025.108431

Experimental method

X-RAY DIFFRACTION (2.1 Å)