3O06

Crystal Structure of yeast pyridoxal 5-phosphate synthase Snz1

Summary for 3O06

• Entry DOI: 10.2210/pdb3o06/pdb
• Related: 1znn 2zbt 3O05 3O07 3fem
• Descriptor: Pyridoxine biosynthesis protein SNZ1 (2 entities in total)
• Functional Keywords: (beta/alpha)8-barrel, pyridoxal 5-phosphate synthase, plp sno1 g3p r5p, biosynthetic protein
• Biological source: Saccharomyces cerevisiae (yeast)
• Total number of polymer chains: 3
• Total formula weight: 94098.84

Authors

Teng, Y.B.,Zhang, X.,Zhou, C.Z.,Hu, H.X. (deposition date: 2010-07-19, release date: 2010-11-24, Last modification date: 2023-11-01)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.35 Å)