6LIU

Crystal structure of apo Tyrosine decarboxylase

Summary for 6LIU

• Entry DOI: 10.2210/pdb6liu/pdb
• Descriptor: Tyrosine/DOPA decarboxylase 2 (2 entities in total)
• Functional Keywords: apo form, decarboxylase, plp binding, tyrosine, lyase
• Biological source: Papaver somniferum (Opium poppy)
• Total number of polymer chains: 6
• Total formula weight: 356541.61

Authors

Yu, J.,Wang, H.,Yao, M. (deposition date: 2019-12-13, release date: 2020-02-12, Last modification date: 2024-05-01)

Primary citation

Wang, H.,Yu, J.,Satoh, Y.,Nakagawa, Y.,Tanaka, R.,Kato, K.,Yao, M.
Crystal structures clarify cofactor binding of plant tyrosine decarboxylase.
Biochem.Biophys.Res.Commun., 2019

PubMed Abstract: Plant tyrosine decarboxylase (TyrDC) is a group II pyridoxal 5'-phosphate (PLP)-dependent decarboxylase that mainly catalyzes the decarboxylation of tyrosine to tyramine. This is biologically important for diverting essential primary metabolites into secondary metabolic pathways. Intensive studies have characterized the effective of PLP-binding and the substrate specificity of mammalian 3,4-dihydroxyphenyl-l-alanine (Dopa) decarboxylases, a member of group II PLP-dependent decarboxylase. However, the characteristics of PLP binding and substrate specificity of plant TyrDCs remain unknown. In this study, we focus on the PLP binding manner, and determined the crystal structures of the apo and PLP binding form of type II TyrDC from Papaver somniferum (PsTyrDCII and PsTyrDCII-PLP). The structures showed that, unlike mammalian Dopa decarboxylase, the binding of PLP does not induce distinct conformational changes of PsTyrDCII regarding the overall structure, but the PLP binding pocket displays conformational changes at Phe124, His203 and Thr262. Combining structural comparation and the obtained biochemical findings, it is demonstrated that PsTyrDCII does not binds PLP tightly. Such characteristics of PLP binding may be required by its catalytic reaction and substrate binding. The activity of TyrDC probably regulated by the concentration of PLP in cells.

PubMed: 31898973
DOI: 10.1016/j.bbrc.2019.12.077

Experimental method

X-RAY DIFFRACTION (2.8 Å)