X-ray crystallography–based structural elucidation of enzyme-bound intermediates along the 1-deoxy-D-xylulose 5-phosphate synthase reaction coordinate

Percival Yang Ting Chen, Alicia A. DeColli, Caren L Meyers, Catherine L. Drennan

Research output: Contribution to journalArticle

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-phos-phate (DXP), an essential bacterial metabolite. DXP is not utilized by humans; hence, DXPS has been an attractive antibacterial target. Here, we investigate DXPS from Deinococcus radiodurans (DrDXPS), showing that it has similar kinetic parameters Km D-GAP AND Km pyruvate (54 3 and 11 1 M, respectively) and comparable catalytic activity (kcat 45 2 min1) 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 DrDXPS in two states along the reaction coordinate: a structure of DrDXPS bound to C2-phosphonolactylThDP (PLThDP), mimicking the native pre-decarboxylation intermediate C2-lactylThDP (LThDP), and a native post-decarboxylation state with a bound enamine intermediate. The 1.94-Å-res-olution structure of PLThDP-bound DrDXPS delineates how two active-site histidine residues stabilize the LThDP intermediate. Meanwhile, the 2.40-Å-resolution structure of an enamine intermediate-bound DrDXPS 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.

Original languageEnglish (US)
Pages (from-to)12405-12414
Number of pages10
JournalJournal of Biological Chemistry
Volume294
Issue number33
DOIs
StatePublished - Jan 1 2019

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Decarboxylation
X-Rays
X rays
Xylulose
Glyceraldehyde 3-Phosphate
Enzymes
Pyruvic Acid
Histidine
Catalytic Domain
Deinococcus
Thiamine Pyrophosphate
Metabolites
Kinetic parameters
Catalyst activity
deoxyxylulose-5-phosphate synthase
Substrates
Proteins

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

X-ray crystallography–based structural elucidation of enzyme-bound intermediates along the 1-deoxy-D-xylulose 5-phosphate synthase reaction coordinate. / Chen, Percival Yang Ting; DeColli, Alicia A.; Meyers, Caren L; Drennan, Catherine L.

In: Journal of Biological Chemistry, Vol. 294, No. 33, 01.01.2019, p. 12405-12414.

Research output: Contribution to journalArticle

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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-phos-phate (DXP), an essential bacterial metabolite. DXP is not utilized by humans; hence, DXPS has been an attractive antibacterial target. Here, we investigate DXPS from Deinococcus radiodurans (DrDXPS), showing that it has similar kinetic parameters Km D-GAP AND Km pyruvate (54 3 and 11 1 M, respectively) and comparable catalytic activity (kcat 45 2 min1) 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 DrDXPS in two states along the reaction coordinate: a structure of DrDXPS bound to C2-phosphonolactylThDP (PLThDP), mimicking the native pre-decarboxylation intermediate C2-lactylThDP (LThDP), and a native post-decarboxylation state with a bound enamine intermediate. The 1.94-{\AA}-res-olution structure of PLThDP-bound DrDXPS delineates how two active-site histidine residues stabilize the LThDP intermediate. Meanwhile, the 2.40-{\AA}-resolution structure of an enamine intermediate-bound DrDXPS reveals how a previously unknown 17-{\AA} 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.",
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