6OUV

1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Deinococcus radiodurans with methylacetylphosphonate (MAP) bound

Summary for 6OUV

• Entry DOI: 10.2210/pdb6ouv/pdb
• Related: 6OUW
• Descriptor: 1-deoxy-D-xylulose-5-phosphate synthase, 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1S)-1-HYDROXY-1-[(R)-HYDROXY(METHOXY)PHOSPHORYL]ETHYL}-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: 1-deoxy-d-xylulose 5-phosphate synthase, dxps, thiamine diphosphate, thiamine pyrophosphate, thdp, tpp, changes, the mep pathway, transferase
• Biological source: Deinococcus radiodurans
• Total number of polymer chains: 2
• Total formula weight: 141280.35

Authors

Chen, P.Y.-T.,Drennan, C.L. (deposition date: 2019-05-05, release date: 2019-07-03, Last modification date: 2023-10-11)

Primary citation

Chen, P.Y.,DeColli, A.A.,Freel Meyers, C.L.,Drennan, C.L.
X-ray crystallography-based structural elucidation of enzyme-bound intermediates along the 1-deoxy-d-xylulose 5-phosphate synthase reaction coordinate.
J.Biol.Chem., 294:12405-12414, 2019

PubMed Abstract: 1-Deoxy-d-xylulose 5-phosphate synthase (DXPS) uses thiamine diphosphate (ThDP) to convert pyruvate and d-glyceraldehyde 3-phosphate (d-GAP) into 1-deoxy-d-xylulose 5-phosphate (DXP), an essential bacterial metabolite. DXP is not utilized by humans; hence, DXPS has been an attractive antibacterial target. Here, we investigate DXPS from (DXPS), showing that it has similar kinetic parameters and (54 ± 3 and 11 ± 1 μm, respectively) and comparable catalytic activity ( = 45 ± 2 min) with previously studied bacterial DXPS enzymes and employing it to obtain missing structural data on this enzyme family. In particular, we have determined crystallographic snapshots of DXPS in two states along the reaction coordinate: a structure of DXPS bound to C2α-phosphonolactylThDP (PLThDP), mimicking the native pre-decarboxylation intermediate C2α-lactylThDP (LThDP), and a native post-decarboxylation state with a bound enamine intermediate. The 1.94-Å-resolution structure of PLThDP-bound DXPS delineates how two active-site histidine residues stabilize the LThDP intermediate. Meanwhile, the 2.40-Å-resolution structure of an enamine intermediate-bound DXPS reveals how a previously unknown 17-Å conformational change removes one of the two histidine residues from the active site, likely triggering LThDP decarboxylation to form the enamine intermediate. These results provide insight into how the bi-substrate enzyme DXPS limits side reactions by arresting the reaction on the less reactive LThDP intermediate when its cosubstrate is absent. They also offer a molecular basis for previous low-resolution experimental observations that correlate decarboxylation of LThDP with protein conformational changes.

PubMed: 31239351
DOI: 10.1074/jbc.RA119.009321

Experimental method

X-RAY DIFFRACTION (1.937 Å)