PMID:22792278

Citation	Griffin, MD, Billakanti, JM, Wason, A, Keller, S, Mertens, HD, Atkinson, SC, Dobson, RC, Perugini, MA, Gerrard, JA and Pearce, FG (2012) Characterisation of the first enzymes committed to lysine biosynthesis in Arabidopsis thaliana. PLoS ONE 7:e40318
Abstract	In plants, the lysine biosynthetic pathway is an attractive target for both the development of herbicides and increasing the nutritional value of crops given that lysine is a limiting amino acid in cereals. Dihydrodipicolinate synthase (DHDPS) and dihydrodipicolinate reductase (DHDPR) catalyse the first two committed steps of lysine biosynthesis. Here, we carry out for the first time a comprehensive characterisation of the structure and activity of both DHDPS and DHDPR from Arabidopsis thaliana. The A. thaliana DHDPS enzyme (At-DHDPS2) has similar activity to the bacterial form of the enzyme, but is more strongly allosterically inhibited by (S)-lysine. Structural studies of At-DHDPS2 show (S)-lysine bound at a cleft between two monomers, highlighting the allosteric site; however, unlike previous studies, binding is not accompanied by conformational changes, suggesting that binding may cause changes in protein dynamics rather than large conformation changes. DHDPR from A. thaliana (At-DHDPR2) has similar specificity for both NADH and NADPH during catalysis, and has tighter binding of substrate than has previously been reported. While all known bacterial DHDPR enzymes have a tetrameric structure, analytical ultracentrifugation, and scattering data unequivocally show that At-DHDPR2 exists as a dimer in solution. The exact arrangement of the dimeric protein is as yet unknown, but ab initio modelling of x-ray scattering data is consistent with an elongated structure in solution, which does not correspond to any of the possible dimeric pairings observed in the X-ray crystal structure of DHDPR from other organisms. This increased knowledge of the structure and function of plant lysine biosynthetic enzymes will aid future work aimed at improving primary production.
Links	PubMed PMC3390394 Online version:10.1371/journal.pone.0040318
Keywords	Allosteric Site; Arabidopsis/enzymology; Arabidopsis/metabolism; Arabidopsis Proteins/chemistry; Biosynthetic Pathways; Crystallography, X-Ray; Dihydrodipicolinate Reductase/chemistry; Hydro-Lyases/chemistry; Kinetics; Light; Lysine/biosynthesis; Models, Molecular; Protein Interaction Domains and Motifs; Protein Structure, Quaternary; Scattering, Small Angle; Structural Homology, Protein
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
ARATH:DAPA2		GO:0008840: 4-hydroxy-tetrahydrodipicolinate synthase	ECO:0000314:		F		Fig S2	complete CACAO 7786
ARATH:DAPA2	enables	GO:0008840: 4-hydroxy-tetrahydrodipicolinate synthase	ECO:0000314: direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
ARATH:DAPB1		GO:0008839: 4-hydroxy-tetrahydrodipicolinate reductase	ECO:0000314:		F		table 1	complete CACAO 7784
ARATH:DAPB1	enables	GO:0008839: 4-hydroxy-tetrahydrodipicolinate reductase	ECO:0000314: direct assay evidence used in manual assertion		F		Seeded From UniProt	complete

References

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