X-ray structure determination of Trypanosoma brucei ornithine decarboxylase bound to D-ornithine and to G418 insights into substrate binding and odc conformational flexibility

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Abstract

Ornithine decarboxylase (ODC) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that catalyzes the rate-determining step in the biosynthesis of polyamines. ODC is a proven drug target to treat African sleeping sickness. The x-ray crystal structure of Trypanosoma brucei ODC in complex with D-ornithine (D-Orn), a substrate analog, and G418 (Geneticin), a weak non-competitive inhibitor, was determined to 2.5-Å resolution. D-Orn forms a Schiff base with PLP, and the side chain is in a similar position to that observed for putrescine and α-difluoromethylornithine in previous T. brucei ODC structures. The D-Orn carboxylate is positioned on the solvent-exposed side of the active site (si face of PLP), and Gly-199, Gly-362, and His-197 are the only residues within 4.2 Å of this moiety. This structure confirms predictions that the carboxylate of D-Orn binds on the si face of PLP, and it supports a model in which the carboxyl group of the substrate L-Orn would be buried on the re face of the cofactor in a pocket that includes Phe-397, Tyr-389, Lys-69 (methylene carbons), and Asp-361. Electron density for G418 was observed at the boundary between the two domains within each ODC monomer. A ten-amino acid loop region (392-401) near the 2-fold axis of the dimer interface, which contributes several residues that form the active site, is disordered in this structure. The disordering of residues in the active site provides a potential mechanism for inhibition by G418 and suggests that allosteric inhibition from this site is feasible.

Original languageEnglish (US)
Pages (from-to)22037-22043
Number of pages7
JournalJournal of Biological Chemistry
Volume278
Issue number24
DOIs
StatePublished - Jun 13 2003

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Trypanosoma brucei brucei
Ornithine
Ornithine Decarboxylase
Pyridoxal Phosphate
X-Rays
X rays
Substrates
Catalytic Domain
Allosteric Site
African Trypanosomiasis
Eflornithine
Putrescine
Schiff Bases
Biosynthesis
Polyamines
Dimers
Carrier concentration
Carbon
Monomers
Crystal structure

ASJC Scopus subject areas

  • Biochemistry

Cite this

@article{eebe7629cf1845de83d8df0bb8f6ab46,
title = "X-ray structure determination of Trypanosoma brucei ornithine decarboxylase bound to D-ornithine and to G418 insights into substrate binding and odc conformational flexibility",
abstract = "Ornithine decarboxylase (ODC) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that catalyzes the rate-determining step in the biosynthesis of polyamines. ODC is a proven drug target to treat African sleeping sickness. The x-ray crystal structure of Trypanosoma brucei ODC in complex with D-ornithine (D-Orn), a substrate analog, and G418 (Geneticin), a weak non-competitive inhibitor, was determined to 2.5-{\AA} resolution. D-Orn forms a Schiff base with PLP, and the side chain is in a similar position to that observed for putrescine and α-difluoromethylornithine in previous T. brucei ODC structures. The D-Orn carboxylate is positioned on the solvent-exposed side of the active site (si face of PLP), and Gly-199, Gly-362, and His-197 are the only residues within 4.2 {\AA} of this moiety. This structure confirms predictions that the carboxylate of D-Orn binds on the si face of PLP, and it supports a model in which the carboxyl group of the substrate L-Orn would be buried on the re face of the cofactor in a pocket that includes Phe-397, Tyr-389, Lys-69 (methylene carbons), and Asp-361. Electron density for G418 was observed at the boundary between the two domains within each ODC monomer. A ten-amino acid loop region (392-401) near the 2-fold axis of the dimer interface, which contributes several residues that form the active site, is disordered in this structure. The disordering of residues in the active site provides a potential mechanism for inhibition by G418 and suggests that allosteric inhibition from this site is feasible.",
author = "Jackson, {Laurie K.} and Goldsmith, {Elizabeth J.} and Phillips, {Margaret A.}",
year = "2003",
month = "6",
day = "13",
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language = "English (US)",
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pages = "22037--22043",
journal = "Journal of Biological Chemistry",
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T1 - X-ray structure determination of Trypanosoma brucei ornithine decarboxylase bound to D-ornithine and to G418 insights into substrate binding and odc conformational flexibility

AU - Jackson, Laurie K.

AU - Goldsmith, Elizabeth J.

AU - Phillips, Margaret A.

PY - 2003/6/13

Y1 - 2003/6/13

N2 - Ornithine decarboxylase (ODC) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that catalyzes the rate-determining step in the biosynthesis of polyamines. ODC is a proven drug target to treat African sleeping sickness. The x-ray crystal structure of Trypanosoma brucei ODC in complex with D-ornithine (D-Orn), a substrate analog, and G418 (Geneticin), a weak non-competitive inhibitor, was determined to 2.5-Å resolution. D-Orn forms a Schiff base with PLP, and the side chain is in a similar position to that observed for putrescine and α-difluoromethylornithine in previous T. brucei ODC structures. The D-Orn carboxylate is positioned on the solvent-exposed side of the active site (si face of PLP), and Gly-199, Gly-362, and His-197 are the only residues within 4.2 Å of this moiety. This structure confirms predictions that the carboxylate of D-Orn binds on the si face of PLP, and it supports a model in which the carboxyl group of the substrate L-Orn would be buried on the re face of the cofactor in a pocket that includes Phe-397, Tyr-389, Lys-69 (methylene carbons), and Asp-361. Electron density for G418 was observed at the boundary between the two domains within each ODC monomer. A ten-amino acid loop region (392-401) near the 2-fold axis of the dimer interface, which contributes several residues that form the active site, is disordered in this structure. The disordering of residues in the active site provides a potential mechanism for inhibition by G418 and suggests that allosteric inhibition from this site is feasible.

AB - Ornithine decarboxylase (ODC) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that catalyzes the rate-determining step in the biosynthesis of polyamines. ODC is a proven drug target to treat African sleeping sickness. The x-ray crystal structure of Trypanosoma brucei ODC in complex with D-ornithine (D-Orn), a substrate analog, and G418 (Geneticin), a weak non-competitive inhibitor, was determined to 2.5-Å resolution. D-Orn forms a Schiff base with PLP, and the side chain is in a similar position to that observed for putrescine and α-difluoromethylornithine in previous T. brucei ODC structures. The D-Orn carboxylate is positioned on the solvent-exposed side of the active site (si face of PLP), and Gly-199, Gly-362, and His-197 are the only residues within 4.2 Å of this moiety. This structure confirms predictions that the carboxylate of D-Orn binds on the si face of PLP, and it supports a model in which the carboxyl group of the substrate L-Orn would be buried on the re face of the cofactor in a pocket that includes Phe-397, Tyr-389, Lys-69 (methylene carbons), and Asp-361. Electron density for G418 was observed at the boundary between the two domains within each ODC monomer. A ten-amino acid loop region (392-401) near the 2-fold axis of the dimer interface, which contributes several residues that form the active site, is disordered in this structure. The disordering of residues in the active site provides a potential mechanism for inhibition by G418 and suggests that allosteric inhibition from this site is feasible.

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