3OI7

Structure of the structure of the H13A mutant of Ykr043C in complex with sedoheptulose-1,7-bisphosphate

Summary for 3OI7

• Entry DOI: 10.2210/pdb3oi7/pdb
• Related: 3F3K 3LG2 3LL4
• Descriptor: Uncharacterized protein YKR043C, 1,7-di-O-phosphono-beta-D-altro-hept-2-ulofuranose, MAGNESIUM ION, ... (7 entities in total)
• Functional Keywords: beta-furanose, structural genomics, psi-2, protein structure initiative, midwest center for structural genomics, mcsg, alpha-beta, sedoheptulose-1, 7-bisphosphatase, phosphatase, hydrolase
• Biological source: Saccharomyces cerevisiae (yeast)
• Total number of polymer chains: 4
• Total formula weight: 136929.00

Authors

Singer, A.U.,Xu, X.,Dong, A.,Cui, H.,Clasquin, M.F.,Caudy, A.A.,Edwards, A.M.,Savchenko, A.,Joachimiak, A.,Yakunin, A.F.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2010-08-18, release date: 2010-11-17, Last modification date: 2024-11-20)

Primary citation

Clasquin, M.F.,Melamud, E.,Singer, A.,Gooding, J.R.,Xu, X.,Dong, A.,Cui, H.,Campagna, S.R.,Savchenko, A.,Yakunin, A.F.,Rabinowitz, J.D.,Caudy, A.A.
Riboneogenesis in yeast.
Cell(Cambridge,Mass.), 145:969-980, 2011

PubMed Abstract: Glucose is catabolized in yeast via two fundamental routes, glycolysis and the oxidative pentose phosphate pathway, which produces NADPH and the essential nucleotide component ribose-5-phosphate. Here, we describe riboneogenesis, a thermodynamically driven pathway that converts glycolytic intermediates into ribose-5-phosphate without production of NADPH. Riboneogenesis begins with synthesis, by the combined action of transketolase and aldolase, of the seven-carbon bisphosphorylated sugar sedoheptulose-1,7-bisphosphate. In the pathway's committed step, sedoheptulose bisphosphate is hydrolyzed to sedoheptulose-7-phosphate by the enzyme sedoheptulose-1,7-bisphosphatase (SHB17), whose activity we identified based on metabolomic analysis of the corresponding knockout strain. The crystal structure of Shb17 in complex with sedoheptulose-1,7-bisphosphate reveals that the substrate binds in the closed furan form in the active site. Sedoheptulose-7-phosphate is ultimately converted by known enzymes of the nonoxidative pentose phosphate pathway to ribose-5-phosphate. Flux through SHB17 increases when ribose demand is high relative to demand for NADPH, including during ribosome biogenesis in metabolically synchronized yeast cells.

PubMed: 21663798
DOI: 10.1016/j.cell.2011.05.022

Experimental method

X-RAY DIFFRACTION (2.4 Å)