7NHE

Crystal structure of Arabidopsis thaliana Pdx1K166R-I333 complex

Summary for 7NHE

Entry DOI	10.2210/pdb7nhe/pdb
Descriptor	Pyridoxal 5'-phosphate synthase subunit PDX1.3, PHOSPHATE ION, [(~{E},4~{S})-4-azanyl-3-oxidanylidene-pent-1-enyl] dihydrogen phosphate, ... (4 entities in total)
Functional Keywords	vitamin b6 biosythesis, plp synthase, pdx1, lyase
Biological source	Arabidopsis thaliana (Mouse-ear cress)
Total number of polymer chains	4
Total formula weight	126000.61
Authors	Rodrigues, M.J.,Zhang, Y.,Bolton, R.,Evans, G.,Giri, N.,Royant, A.,Begley, T.,Ealick, S.E.,Tews, I. (deposition date: 2021-02-10, release date: 2021-12-22, Last modification date: 2024-10-16)
Primary citation	Rodrigues, M.J.,Giri, N.,Royant, A.,Zhang, Y.,Bolton, R.,Evans, G.,Ealick, S.E.,Begley, T.,Tews, I. Trapping and structural characterisation of a covalent intermediate in vitamin B 6 biosynthesis catalysed by the Pdx1 PLP synthase. Rsc Chem Biol, 3:227-230, 2022 Cited by PubMed Abstract: The Pdx1 enzyme catalyses condensation of two carbohydrates and ammonia to form pyridoxal 5-phosphate (PLP) an imine relay mechanism of carbonyl intermediates. The I intermediate characterised here using structural, UV-vis absorption spectroscopy and mass spectrometry analyses rationalises stereoselective deprotonation and subsequent substrate assisted phosphate elimination, central to PLP biosynthesis. PubMed: 35360887 DOI: 10.1039/d1cb00160d PDB entries with the same primary citation
Experimental method	X-RAY DIFFRACTION (2.23 Å)

Structure validation