Structure of a bacterial pyridoxal 5′-phosphate synthase complex

Abstract

Vitamin B6 is an essential metabolic cofactor that has more functions in humans than any other single nutrient. Its de novo biosynthesis occurs through two mutually exclusive pathways that are absent in animals. The predominant pathway found in most prokaryotes, fungi, and plants has only recently been discovered. It is distinguished by a glutamine amidotransferase, which is remarkable in that it alone can synthesize the cofactor form, pyridoxal 5-phosphate (PLP), directly from a triose and a pentose saccharide and glutamine. Here we report the 3D structure of the PLP synthase complex with substrate glutamine bound as well as those of the individual synthase and glutaminase subunits Pdx1 and Pdx2, respectively. The complex is made up of 24 protein units assembled like a cogwheel, a dodecameric Pdx1 to which 12 Pdx2 subunits attach. In contrast to the architecture of previously determined glutamine amidotransferases, macromolecular assembly is directed by an N-terminal ␣-helix on the synthase. Interaction with the synthase subunit leads to glutaminase activation, resulting in formation of an oxyanion hole, a prerequisite for catalysis. Mutagenesis permitted identification of the remote glutaminase and synthase catalytic centers and led us to propose a mechanism whereby ammonia shuttles between these active sites through a methionine-rich hydrophobic tunnel.3D structure ͉ ammonia tunnel ͉ glutamine amidotransferase ͉ oxyanion ͉ vitamin B6

Crystal Structure of Pyridoxal Biosynthesis Lyase PdxS from Pyrococcus horikoshii

“…The structure suggests that an oxyanion hole is formed in the active site of PdxT triggered by a peptide flip induced by interaction with PdxS (Strohmeier et al, 2006). The ammonia produced from the hydrolysis of glutamine by PdxT travels through an internal tunnel in the PdxS to reach the active site (Strohmeier et al, 2006). The crystal structures of Saccharomyces cerevisiae Snz1 (apo-, Snz1-G3P complex, and Snz1-PLP complex) have also been reported (Zhang et al, 2010).…”

“…The active site of G. stearothermophilus PdxS, a pair of hexameric rings, is positioned on the inside of the dodecamer (Zhu et al, 2005). The crystal structures of Thermotoga maritima YaaD-YaaE complex bound with RBP and the Bacillus subtilis Pdx1-Pdx2 complex have also been reported (Strohmeier et al, 2006;Zein et al, 2006). Both Pdx1-Pdx2 and YaaD-YaaE complexes are made up of 24 subunits consisting of a dodecameric Pdx1 (or YaaD) and Pdx2 (or YaaE) (Strohmeier et al, 2006;Zein et al, 2006).…”

“…The crystal structures of Thermotoga maritima YaaD-YaaE complex bound with RBP and the Bacillus subtilis Pdx1-Pdx2 complex have also been reported (Strohmeier et al, 2006;Zein et al, 2006). Both Pdx1-Pdx2 and YaaD-YaaE complexes are made up of 24 subunits consisting of a dodecameric Pdx1 (or YaaD) and Pdx2 (or YaaE) (Strohmeier et al, 2006;Zein et al, 2006). The glutaminase PdxT (Pdx2, YaaE) is inactive in the absence of the synthase subunit PdxS (Strohmeier et al, 2006;Zein et al, 2006;Zhu et al, 2005).…”

“…Both Pdx1-Pdx2 and YaaD-YaaE complexes are made up of 24 subunits consisting of a dodecameric Pdx1 (or YaaD) and Pdx2 (or YaaE) (Strohmeier et al, 2006;Zein et al, 2006). The glutaminase PdxT (Pdx2, YaaE) is inactive in the absence of the synthase subunit PdxS (Strohmeier et al, 2006;Zein et al, 2006;Zhu et al, 2005). The structure suggests that an oxyanion hole is formed in the active site of PdxT triggered by a peptide flip induced by interaction with PdxS (Strohmeier et al, 2006).…”

“…The glutaminase PdxT (Pdx2, YaaE) is inactive in the absence of the synthase subunit PdxS (Strohmeier et al, 2006;Zein et al, 2006;Zhu et al, 2005). The structure suggests that an oxyanion hole is formed in the active site of PdxT triggered by a peptide flip induced by interaction with PdxS (Strohmeier et al, 2006). The ammonia produced from the hydrolysis of glutamine by PdxT travels through an internal tunnel in the PdxS to reach the active site (Strohmeier et al, 2006).…”