1PVY

3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii in complex with ribulose 5-phosphate

Summary for 1PVY

• Entry DOI: 10.2210/pdb1pvy/pdb
• Related: 1PVW
• Descriptor: 3,4-dihydroxy-2-butanone 4-phosphate synthase, RIBULOSE-5-PHOSPHATE, ZINC ION, ... (5 entities in total)
• Functional Keywords: riboflavin biosynthesis, isomerase
• Biological source: Methanocaldococcus jannaschii
• Total number of polymer chains: 2
• Total formula weight: 52379.86

Authors

Steinbacher, S.,Schiffmann, S.,Richter, G.,Huber, R.,Bacher, A.,Fischer, M. (deposition date: 2003-06-29, release date: 2003-11-04, Last modification date: 2023-10-25)

Primary citation

Steinbacher, S.,Schiffmann, S.,Richter, G.,Huber, R.,Bacher, A.,Fischer, M.
Structure of 3,4-Dihydroxy-2-butanone 4-Phosphate Synthase from Methanococcus jannaschii in Complex with Divalent Metal Ions and the Substrate Ribulose 5-Phosphate: IMPLICATIONS FOR THE CATALYTIC MECHANISM
J.Biol.Chem., 278:42256-42265, 2003

PubMed Abstract: Skeletal rearrangements of carbohydrates are crucial for many biosynthetic pathways. In riboflavin biosynthesis ribulose 5-phosphate is converted into 3,4-dihydroxy-2-butanone 4-phosphate while its C4 atom is released as formate in a sequence of metal-dependent reactions. Here, we present the crystal structure of Methanococcus jannaschii 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with the substrate ribulose 5-phosphate at a dimetal center presumably consisting of non-catalytic zinc and calcium ions at 1.7-A resolution. The carbonyl group (O2) and two out of three free hydroxyl groups (OH3 and OH4) of the substrate are metal-coordinated. We correlate previous mutational studies on this enzyme with the present structural results. Residues of the first coordination sphere involved in metal binding are indispensable for catalytic activity. Only Glu-185 of the second coordination sphere cannot be replaced without complete loss of activity. It contacts the C3 hydrogen atom directly and probably initiates enediol formation in concert with both metal ions to start the reaction sequence. Mechanistic similarities to Rubisco acting on the similar substrate ribulose 1,5-diphosphate in carbon dioxide fixation as well as other carbohydrate (reducto-) isomerases are discussed.

PubMed: 12904291
DOI: 10.1074/jbc.M307301200

Experimental method

X-RAY DIFFRACTION (1.7 Å)