6OOC

Structure of the pterocarpan synthase dirigent protein GePTS1

Summary for 6OOC

• Entry DOI: 10.2210/pdb6ooc/pdb
• Descriptor: Dirigent protein (2 entities in total)
• Functional Keywords: dirigent protein, apo-form, plant protein
• Biological source: Glycyrrhiza echinata (Licorice)
• Total number of polymer chains: 6
• Total formula weight: 145589.00

Authors

Smith, C.A. (deposition date: 2019-04-23, release date: 2020-04-29, Last modification date: 2023-10-11)

Primary citation

Meng, Q.,Moinuddin, S.G.A.,Kim, S.J.,Bedgar, D.L.,Costa, M.A.,Thomas, D.G.,Young, R.P.,Smith, C.A.,Cort, J.R.,Davin, L.B.,Lewis, N.G.
Pterocarpan synthase (PTS) structures suggest a common quinone methide-stabilizing function in dirigent proteins and proteins with dirigent-like domains.
J.Biol.Chem., 295:11584-11601, 2020

PubMed Abstract: The biochemical activities of dirigent proteins (DPs) give rise to distinct complex classes of plant phenolics. DPs apparently began to emerge during the aquatic-to-land transition, with phylogenetic analyses revealing the presence of numerous DP subfamilies in the plant kingdom. The vast majority (>95%) of DPs in these large multigene families still await discovery of their biochemical functions. Here, we elucidated the 3D structures of two pterocarpan-forming proteins with dirigent-like domains. Both proteins stereospecifically convert distinct diastereomeric chiral isoflavonoid precursors to the chiral pterocarpans, (-)- and (+)-medicarpin, respectively. Their 3D structures enabled comparisons with stereoselective lignan- and aromatic terpenoid-forming DP orthologs. Each protein provides entry into diverse plant natural products classes, and our experiments suggest a common biochemical mechanism in binding and stabilizing distinct plant phenol-derived mono- and bis-quinone methide intermediates during different C-C and C-O bond-forming processes. These observations provide key insights into both their appearance and functional diversification of DPs during land plant evolution/adaptation. The proposed biochemical mechanisms based on our findings provide important clues to how additional physiological roles for DPs and proteins harboring dirigent-like domains can now be rationally and systematically identified.

PubMed: 32565424
DOI: 10.1074/jbc.RA120.012444

Experimental method

X-RAY DIFFRACTION (2.6 Å)