Crystal Structure of Pyridoxal Biosynthesis Lyase PdxS from Pyrococcus horikoshii

Structural definition of the lysine swing in Arabidopsis thaliana PDX1: Intermediate channeling facilitating vitamin B 6 biosynthesis

“…3B). In an analogous fashion, another short helix, α8′, adopts an outward and inward position over the P1 site dependent on the absence or presence of substrate, respectively (11,18,32). Here we observe that this helix is in the inward conformation in PDX1.3 ( Fig.…”

“…2B). As for the homologous counterparts of PDX1.3, the bound sulfates in P1 and P2 occupy the same position as the phosphates of bound R5P and PLP, respectively (11,15,17,18,32). Markedly, except for coordinated waters, there is no other density observed in the P1 or P2 sites, such that this structural snapshot of the PDX1.3 enzyme can be considered substrate and product free, i.e., apo-PDX1.…”

“…Nevertheless, it is hypothesized that this residue couples the P1 and P2 active sites by a swinging arm mechanism pivoting between the two sites. However, with the exception of the most recently described structure of the G. stearothermophilus enzyme (15), it has been exclusively observed oriented toward the P2 site, regardless of the presence or absence of substrate (R5P) or product (PLP) in both prokaryotic and eukaryotic structures (11,15,17,18,32). Thus, orientation of this lysine residue toward the P2 site presumably represents the resting state.…”

“…However, α2′ has since been observed in the reported structure of PDX1 alone from the archaeon P. horikoshii (4FIQ and 4FIR) (32), as well as in the eukaryotic PDX1 structures reported from S. cerevisiae (3FEM, 3O05, 3O06, and 3O07) (13,18) and Plasmodium berghei (4ADT and 4ADU) (11), all of which were crystallized in the absence of PDX2. Furthermore, in the archaeal and eukaryotic structures, α2′ exists in either of two conformations (out or in), dependent on the absence or presence of R5P, respectively (11,18,32). In the presence of the substrate, the inward movement of α2′ partially covers the solvent accessible P1 active site.…”

“…Two active sites, annotated P1 and P2, have been definitively located in PDX1 enzymes (16,17). These sites were originally defined by bound chloride, phosphate, or sulfate ions in X-ray crystallographic structures (16,17,29) and more recently by the bound substrate R5P (P1) and product PLP (P2) (11,18,32) and have been validated through several biochemical studies (10,12,16). In PDX1.3, the P1 site is located at the C-terminal mouth of the β-barrel and contains density for a sulfate ion surrounded by the characteristic phosphate-binding loop that includes Gly-ThrGly, as well as other established conserved residues of this active site (16,29) (Fig.…”