6P3M

Tetrahydroprotoberberine N-methyltransferase in complex with S-adenosylhomocysteine

Summary for 6P3M

• Entry DOI: 10.2210/pdb6p3m/pdb
• Descriptor: tetrahydroprotoberberine N-methyltransferase, S-ADENOSYL-L-HOMOCYSTEINE, SULFATE ION, ... (4 entities in total)
• Functional Keywords: methyltransferase, transferase
• Biological source: Glaucium flavum
• Total number of polymer chains: 1
• Total formula weight: 44282.40

Authors

Lang, D.E.,Morris, J.S.,Rowley, M.,Torres, M.A.,Maksimovich, V.A.,Facchini, P.J.,Ng, K.K.S. (deposition date: 2019-05-24, release date: 2019-08-14, Last modification date: 2023-10-11)

Primary citation

Lang, D.E.,Morris, J.S.,Rowley, M.,Torres, M.A.,Maksimovich, V.A.,Facchini, P.J.,Ng, K.K.S.
Structure-function studies of tetrahydroprotoberberineN-methyltransferase reveal the molecular basis of stereoselective substrate recognition.
J.Biol.Chem., 294:14482-14498, 2019

PubMed Abstract: Benzylisoquinoline alkaloids (BIAs) are a structurally diverse class of plant-specialized metabolites that have been particularly well-studied in the order Ranunculales. The -methyltransferases (NMTs) in BIA biosynthesis can be divided into three groups according to substrate specificity and amino acid sequence. Here, we report the first crystal structures of enzyme complexes from the tetrahydroprotoberberine NMT (TNMT) subclass, specifically for TNMT from the yellow horned poppy (). TNMT was co-crystallized with the cofactor -adenosyl-l-methionine ( = 1.6 Å), the product -adenosyl-l-homocysteine ( = 1.8 Å), or in complex with -adenosyl-l-homocysteine and ()--methylstylopine = 1.8 Å). These structures reveal for the first time how a mostly hydrophobic L-shaped substrate recognition pocket selects for the ()- configuration of the two central six-membered rings in protoberberine BIA compounds. Mutagenesis studies confirm and functionally define the roles of several highly-conserved residues within and near the TNMT-active site. The substrate specificity of TNMT enzymes appears to arise from the arrangement of subgroup-specific stereospecific recognition elements relative to catalytic elements that are more widely-conserved among all BIA NMTs. The binding mode of protoberberine compounds to TNMT appears to be similar to coclaurine NMT, with the isoquinoline rings buried deepest in the binding pocket. This binding mode differs from that of pavine NMT, in which the benzyl ring is bound more deeply than the isoquinoline rings. The insights into substrate recognition and catalysis provided here form a sound basis for the rational engineering of NMT enzymes for chemoenzymatic synthesis and metabolic engineering.

PubMed: 31395658
DOI: 10.1074/jbc.RA119.009214

Experimental method

X-RAY DIFFRACTION (1.8 Å)