6CD0

Crystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3), PLP-internal aldimine and apo form

Summary for 6CD0

• Entry DOI: 10.2210/pdb6cd0/pdb
• Descriptor: Serine hydroxymethyltransferase, ACETATE ION, FORMIC ACID, ... (5 entities in total)
• Functional Keywords: plp, one-carbon cycle, tetrahydrofolate, chloroplast, tetramer, transferase
• Biological source: Medicago truncatula (Barrel medic); More
• Total number of polymer chains: 4
• Total formula weight: 199399.46

Authors

Ruszkowski, M.,Sekula, B.,Ruszkowska, A.,Dauter, Z. (deposition date: 2018-02-07, release date: 2018-05-23, Last modification date: 2023-11-15)

Primary citation

Ruszkowski, M.,Sekula, B.,Ruszkowska, A.,Dauter, Z.
Chloroplastic Serine Hydroxymethyltransferase FromMedicago truncatula: A Structural Characterization.
Front Plant Sci, 9:584-584, 2018

PubMed Abstract: Serine hydroxymethyltransferase (SHMT, EC 2.1.2.1) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme which catalyzes the reversible serine-to-glycine conversion in either a tetrahydrofolate-dependent or -independent manner. The enzyme is also responsible for the tetrahydrofolate-independent cleavage of other β-hydroxy amino acids. In addition to being an essential player in the serine homeostasis, SHMT action is the main source of activated one-carbon units, which links SHMT activity with the control of cell proliferation. In plants, studies of SHMT enzymes are more complicated than of those of, e.g., bacterial or mammalian origins because plant genomes encode multiple SHMT isozymes that are targeted to different subcellular compartments: cytosol, mitochondria, plastids, and nucleus. Here we report crystal structures of chloroplast-targeted SHMT from (SHMT3). SHMT3 is a tetramer in solution, composed of two tight and obligate dimers. Our complexes with PLP internal aldimine, PLP-serine and PLP-glycine external aldimines, and PLP internal aldimine with a free glycine reveal structural details of the SHMT3-catalyzed reaction. Capturing the enzyme in different stages along the course of the slow tetrahydrofolate-independent serine-to-glycine conversion allowed to observe a unique conformation of the PLP-serine γ-hydroxyl group, and a concerted movement of two tyrosine residues in the active site.

PubMed: 29868052
DOI: 10.3389/fpls.2018.00584

Experimental method

X-RAY DIFFRACTION (1.74 Å)