Conformational changes in orotidine 5′-monophosphate decarboxylase

A structure-based explanation for how the 5′-phosphate group activates the enzyme

Bijoy J. Desai, B. Mc Kay Wood, Alexander A. Fedorov, Elena V. Fedorov, Bogdana Goryanova, Tina L. Amyes, John P. Richard, Steven C. Almo, John Alan Gerlt

Research output: Contribution to journalArticle

Abstract

The binding of a ligand to orotidine 5′-monophosphate decarboxylase (OMPDC) is accompanied by a conformational change from an open, inactive conformation (Eo) to a closed, active conformation (Ec). As the substrate traverses the reaction coordinate to form the stabilized vinyl carbanion/carbene intermediate, interactions that destabilize the carboxylate group of the substrate and stabilize the intermediate (in the E c•S complex) are enforced. Focusing on the OMPDC from Methanothermobacter thermautotrophicus, we find the "remote" 5′-phosphate group of the substrate activates the enzyme 2.4 × 108-fold; the activation is equivalently described by an intrinsic binding energy (IBE) of 11.4 kcal/mol. We studied residues in the activation that (1) directly contact the 5′-phosphate group, (2) participate in a hydrophobic cluster near the base of the active site loop that sequesters the bound substrate from the solvent, and (3) form hydrogen bonding interactions across the interface between the "mobile" and "fixed" half-barrel domains of the (β/α)8-barrel structure. Our data support a model in which the IBE provided by the 5′-phosphate group is used to allow interactions both near the N-terminus of the active site loop and across the domain interface that stabilize both the Ec•S and Ec•S complexes relative to the Eo•S complex. The conclusion that the IBE of the 5′-phosphate group provides stabilization to both the E c•S and Ec•S complexes, not just the Ec•S complex, is central to understanding the structural origins of enzymatic catalysis as well as the requirements for the de novo design of enzymes that catalyze novel reactions.

Original languageEnglish (US)
Pages (from-to)8665-8678
Number of pages14
JournalBiochemistry
Volume51
Issue number43
DOIs
StatePublished - Oct 30 2012

Fingerprint

Carboxy-Lyases
Binding energy
Phosphates
Substrates
Enzymes
Conformations
Catalytic Domain
Methanobacteriaceae
Chemical activation
Hydrogen Bonding
Catalysis
Hydrogen bonds
Stabilization
Ligands
orotidylic acid

ASJC Scopus subject areas

  • Biochemistry

Cite this

Conformational changes in orotidine 5′-monophosphate decarboxylase : A structure-based explanation for how the 5′-phosphate group activates the enzyme. / Desai, Bijoy J.; Wood, B. Mc Kay; Fedorov, Alexander A.; Fedorov, Elena V.; Goryanova, Bogdana; Amyes, Tina L.; Richard, John P.; Almo, Steven C.; Gerlt, John Alan.

In: Biochemistry, Vol. 51, No. 43, 30.10.2012, p. 8665-8678.

Research output: Contribution to journalArticle

Desai, Bijoy J. ; Wood, B. Mc Kay ; Fedorov, Alexander A. ; Fedorov, Elena V. ; Goryanova, Bogdana ; Amyes, Tina L. ; Richard, John P. ; Almo, Steven C. ; Gerlt, John Alan. / Conformational changes in orotidine 5′-monophosphate decarboxylase : A structure-based explanation for how the 5′-phosphate group activates the enzyme. In: Biochemistry. 2012 ; Vol. 51, No. 43. pp. 8665-8678.
@article{034ae0b39c274d85b835ea48414382ed,
title = "Conformational changes in orotidine 5′-monophosphate decarboxylase: A structure-based explanation for how the 5′-phosphate group activates the enzyme",
abstract = "The binding of a ligand to orotidine 5′-monophosphate decarboxylase (OMPDC) is accompanied by a conformational change from an open, inactive conformation (Eo) to a closed, active conformation (Ec). As the substrate traverses the reaction coordinate to form the stabilized vinyl carbanion/carbene intermediate, interactions that destabilize the carboxylate group of the substrate and stabilize the intermediate (in the E c•S‡ complex) are enforced. Focusing on the OMPDC from Methanothermobacter thermautotrophicus, we find the {"}remote{"} 5′-phosphate group of the substrate activates the enzyme 2.4 × 108-fold; the activation is equivalently described by an intrinsic binding energy (IBE) of 11.4 kcal/mol. We studied residues in the activation that (1) directly contact the 5′-phosphate group, (2) participate in a hydrophobic cluster near the base of the active site loop that sequesters the bound substrate from the solvent, and (3) form hydrogen bonding interactions across the interface between the {"}mobile{"} and {"}fixed{"} half-barrel domains of the (β/α)8-barrel structure. Our data support a model in which the IBE provided by the 5′-phosphate group is used to allow interactions both near the N-terminus of the active site loop and across the domain interface that stabilize both the Ec•S and Ec•S‡ complexes relative to the Eo•S complex. The conclusion that the IBE of the 5′-phosphate group provides stabilization to both the E c•S and Ec•S‡ complexes, not just the Ec•S‡ complex, is central to understanding the structural origins of enzymatic catalysis as well as the requirements for the de novo design of enzymes that catalyze novel reactions.",
author = "Desai, {Bijoy J.} and Wood, {B. Mc Kay} and Fedorov, {Alexander A.} and Fedorov, {Elena V.} and Bogdana Goryanova and Amyes, {Tina L.} and Richard, {John P.} and Almo, {Steven C.} and Gerlt, {John Alan}",
year = "2012",
month = "10",
day = "30",
doi = "10.1021/bi301188k",
language = "English (US)",
volume = "51",
pages = "8665--8678",
journal = "Biochemistry",
issn = "0006-2960",
publisher = "American Chemical Society",
number = "43",

}

TY - JOUR

T1 - Conformational changes in orotidine 5′-monophosphate decarboxylase

T2 - A structure-based explanation for how the 5′-phosphate group activates the enzyme

AU - Desai, Bijoy J.

AU - Wood, B. Mc Kay

AU - Fedorov, Alexander A.

AU - Fedorov, Elena V.

AU - Goryanova, Bogdana

AU - Amyes, Tina L.

AU - Richard, John P.

AU - Almo, Steven C.

AU - Gerlt, John Alan

PY - 2012/10/30

Y1 - 2012/10/30

N2 - The binding of a ligand to orotidine 5′-monophosphate decarboxylase (OMPDC) is accompanied by a conformational change from an open, inactive conformation (Eo) to a closed, active conformation (Ec). As the substrate traverses the reaction coordinate to form the stabilized vinyl carbanion/carbene intermediate, interactions that destabilize the carboxylate group of the substrate and stabilize the intermediate (in the E c•S‡ complex) are enforced. Focusing on the OMPDC from Methanothermobacter thermautotrophicus, we find the "remote" 5′-phosphate group of the substrate activates the enzyme 2.4 × 108-fold; the activation is equivalently described by an intrinsic binding energy (IBE) of 11.4 kcal/mol. We studied residues in the activation that (1) directly contact the 5′-phosphate group, (2) participate in a hydrophobic cluster near the base of the active site loop that sequesters the bound substrate from the solvent, and (3) form hydrogen bonding interactions across the interface between the "mobile" and "fixed" half-barrel domains of the (β/α)8-barrel structure. Our data support a model in which the IBE provided by the 5′-phosphate group is used to allow interactions both near the N-terminus of the active site loop and across the domain interface that stabilize both the Ec•S and Ec•S‡ complexes relative to the Eo•S complex. The conclusion that the IBE of the 5′-phosphate group provides stabilization to both the E c•S and Ec•S‡ complexes, not just the Ec•S‡ complex, is central to understanding the structural origins of enzymatic catalysis as well as the requirements for the de novo design of enzymes that catalyze novel reactions.

AB - The binding of a ligand to orotidine 5′-monophosphate decarboxylase (OMPDC) is accompanied by a conformational change from an open, inactive conformation (Eo) to a closed, active conformation (Ec). As the substrate traverses the reaction coordinate to form the stabilized vinyl carbanion/carbene intermediate, interactions that destabilize the carboxylate group of the substrate and stabilize the intermediate (in the E c•S‡ complex) are enforced. Focusing on the OMPDC from Methanothermobacter thermautotrophicus, we find the "remote" 5′-phosphate group of the substrate activates the enzyme 2.4 × 108-fold; the activation is equivalently described by an intrinsic binding energy (IBE) of 11.4 kcal/mol. We studied residues in the activation that (1) directly contact the 5′-phosphate group, (2) participate in a hydrophobic cluster near the base of the active site loop that sequesters the bound substrate from the solvent, and (3) form hydrogen bonding interactions across the interface between the "mobile" and "fixed" half-barrel domains of the (β/α)8-barrel structure. Our data support a model in which the IBE provided by the 5′-phosphate group is used to allow interactions both near the N-terminus of the active site loop and across the domain interface that stabilize both the Ec•S and Ec•S‡ complexes relative to the Eo•S complex. The conclusion that the IBE of the 5′-phosphate group provides stabilization to both the E c•S and Ec•S‡ complexes, not just the Ec•S‡ complex, is central to understanding the structural origins of enzymatic catalysis as well as the requirements for the de novo design of enzymes that catalyze novel reactions.

UR - http://www.scopus.com/inward/record.url?scp=84868089459&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84868089459&partnerID=8YFLogxK

U2 - 10.1021/bi301188k

DO - 10.1021/bi301188k

M3 - Article

VL - 51

SP - 8665

EP - 8678

JO - Biochemistry

JF - Biochemistry

SN - 0006-2960

IS - 43

ER -