6KHP

Crystal structure of Oryza sativa TDC with PLP and tryptamine

Summary for 6KHP

• Entry DOI: 10.2210/pdb6khp/pdb
• Descriptor: Tryptophan decarboxylase 1, PYRIDOXAL-5'-PHOSPHATE, 2-(1H-INDOL-3-YL)ETHANAMINE, ... (7 entities in total)
• Functional Keywords: amino acid decarboxylase, transferase, lyase
• Biological source: Oryza sativa subsp. japonica (Rice)
• Total number of polymer chains: 2
• Total formula weight: 112671.00

Authors

Zhou, Y.Z.,Liao, L.J.,Liu, X.K.,Guo, Y.,Zhao, Y.C.,Zeng, Z.X. (deposition date: 2019-07-16, release date: 2020-07-15, Last modification date: 2025-04-09)

Primary citation

Zhou, Y.,Liao, L.,Liu, X.,Liu, B.,Chen, X.,Guo, Y.,Huang, C.,Zhao, Y.,Zeng, Z.
Crystal structure ofOryza sativaTDC reveals the substrate specificity for TDC-mediated melatonin biosynthesis.
J Adv Res, 24:501-511, 2020

PubMed Abstract: Plant tryptophan decarboxylase (TDC) is a type II Pyridoxal-5'-phosphate-dependent decarboxylase (PLP_DC) that could be used as a target to genetically improve crops. However, lack of accurate structural information on plant TDC hampers the understanding of its decarboxylation mechanisms. In the present study, the crystal structures of TDC (sTDC) in its complexes with pyridoxal-5'-phosphate, tryptamine and serotonin were determined. The structures provide detailed interaction information between TDC and its substrates. The Y359 residue from the loop gate is a proton donor and forms a Lewis acid-base pair with serotonin/tryptamine, which is associated with product release. The H214 residue is responsible for PLP binding and proton transfer, and its proper interaction with Y359 is essential for TDC enzyme activity. The extra hydrogen bonds formed between the 5-hydroxyl group of serotonin and the backbone carboxyl groups of F104 and P105 explain the discrepancy between the catalytic activity of TDC in tryptophan and in 5-hydroxytryptophan. In addition, an evolutionary analysis revealed that type II PLP_DC originated from glutamic acid decarboxylase, potentially as an adaptive evolution of mechanism in organisms in extreme environments. This study is, to our knowledge, the first to present a detailed analysis of the crystal structure of TDC in these complexes. The information regarding the catalytic mechanism described here could facilitate the development of protocols to regulate melatonin levels and thereby contribute to crop improvement efforts to improve food security worldwide.

PubMed: 32595985
DOI: 10.1016/j.jare.2020.06.004

Experimental method

X-RAY DIFFRACTION (2.299 Å)