3O07

Crystal structure of yeast pyridoxal 5-phosphate synthase Snz1 complexed with substrate G3P

3O07 の概要

• エントリーDOI: 10.2210/pdb3o07/pdb
• 関連するPDBエントリー: 1znn 2zbt 3fem 3o05 3o06
• 分子名称: Pyridoxine biosynthesis protein SNZ1, GLYCERALDEHYDE-3-PHOSPHATE (3 entities in total)
• 機能のキーワード: (beta/alpha)8-barrel, pyridoxal 5-phosphate synthase, plp g3p r5p sno1, biosynthetic protein
• 由来する生物種: Saccharomyces cerevisiae (yeast)
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 94609.01

構造登録者

Teng, Y.B.,Zhang, X.,Hu, H.X.,Zhou, C.Z. (登録日: 2010-07-19, 公開日: 2010-11-24, 最終更新日: 2023-11-01)

主引用文献

Zhang, X.,Teng, Y.B.,Liu, J.P.,He, Y.X.,Zhou, K.,Chen, Y.,Zhou, C.Z.
Structural insights into the catalytic mechanism of the yeast pyridoxal 5-phosphate synthase Snz1
Biochem.J., 432:445-450, 2010

PubMed Abstract: In most eubacteria, fungi, apicomplexa, plants and some metazoans, the active form of vitamin B6, PLP (pyridoxal 5-phosphate), is de novo synthesized from three substrates, R5P (ribose 5-phosphate), DHAP (dihydroxyacetone phosphate) and ammonia hydrolysed from glutamine by a complexed glutaminase. Of the three active sites of DXP (deoxyxylulose 5-phosphate)independent PLP synthase (Pdx1), the R5P isomerization site has been assigned, but the sites for DHAP isomerization and PLP formation remain unknown. In the present study, we present the crystal structures of yeast Pdx1/Snz1, in apo-, G3P (glyceraldehyde 3-phosphate)- and PLP-bound forms, at 2.3, 1.8 and 2.2 Å (1 Å=0.1 nm) respectively. Structural and biochemical analysis enabled us to assign the PLP-formation site, a G3P-binding site and a G3P-transfer site. We propose a putative catalytic mechanism for Pdx1/Snz1 in which R5P and DHAP are isomerized at two distinct sites and transferred along well-defined routes to a final destination for PLP synthesis.

PubMed: 20919991
DOI: 10.1042/BJ20101241

実験手法

X-RAY DIFFRACTION (1.8 Å)