Skip to main content
OSTI.GOVU.S. Department of Energy Office of Scientific and Technical Information
U.S. Department of Energy
Office of Scientific and Technical Information
 

Functional dissection of the bipartite active site of the class I coenzyme A (CoA)-transferase succinyl-CoA:acetate CoA-transferase

Journal Article · · Frontiers in Chemistry
 [1];  [2];  [2]
  1. Purdue Univ., West Lafayette, IN (United States). Dept. of Biochemistry; DOE Office of Scientific and Technical Information (OSTI)
  2. Purdue Univ., West Lafayette, IN (United States). Dept. of Biochemistry
+ Show Author Affiliations
Coenzyme A (CoA)-transferases catalyze the reversible transfer of CoA from acyl-CoA thioesters to free carboxylates. Class I CoA-transferases produce acylglutamyl anhydride intermediates that undergo attack by CoA thiolate on either the internal or external carbonyl carbon atoms, forming distinct tetrahedral intermediates <3 Å apart. Here in this study, crystal structures of succinyl-CoA:acetate CoA-transferase (AarC) from Acetobacter aceti are used to examine how the Asn347 carboxamide stabilizes the internal oxyanion intermediate. A structure of the active mutant AarC-N347A bound to CoA revealed both solvent replacement of the missing contact and displacement of the adjacent Glu294, indicating that Asn347 both polarizes and orients the essential glutamate. AarC was crystallized with the nonhydrolyzable acetyl-CoA (AcCoA) analog dethiaacetyl-CoA (1a) in an attempt to trap a closed enzyme complex containing a stable analog of the external oxyanion intermediate. One active site contained an acetylglutamyl anhydride adduct and truncated 1a, an unexpected result hinting at an unprecedented cleavage of the ketone moiety in 1a. Solution studies confirmed that 1a decomposition is accompanied by production of near-stoichiometric acetate, in a process that seems to depend on microbial contamination but not AarC. A crystal structure of AarC bound to the postulated 1a truncation product (2a) showed complete closure of one active site per dimer but no acetylglutamyl anhydride, even with acetate added. These findings suggest that an activated acetyl donor forms during 1a decomposition; a working hypothesis involving ketone oxidation is offered. Finally, the ability of 2a to induce full active site closure furthermore suggests that it subverts a system used to impede inappropriate active site closure on unacylated CoA.
Research Organization:
Purdue Univ., West Lafayette, IN (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02-06CH11357
OSTI ID:
1345618
Alternate ID(s):
OSTI ID: 1498409
Journal Information:
Frontiers in Chemistry, Journal Name: Frontiers in Chemistry Vol. 4; ISSN 2296-2646
Publisher:
Frontiers Research FoundationCopyright Statement
Country of Publication:
United States
Language:
English

References (56)

Long-term continuous evolution of acetate resistantAcetobacter aceti journal August 2003
Understanding the Acid-Base Properties of Adenosine: The Intrinsic Basicities of N1, N3 and N7 journal May 2011
Chemical approaches to detect and analyze protein sulfenic acids: DETECTION AND ANALYSIS OF SULFENIC ACIDS journal September 2013
On the importance of orientation in general base catalysis by carboxylate journal June 1981
A role for flexible loops in enzyme catalysis journal December 2010
A New Generation of Crystallographic Validation Tools for the Protein Data Bank journal October 2011
Role of Binding Energy with Coenzyme A in Catalysis by 3-Oxoacid Coenzyme A Transferase journal September 1995
Structure of a NADH-Insensitive Hexameric Citrate Synthase that Resists Acid Inactivation † journal November 2006
Crystal Structures of Acetobacter aceti Succinyl-Coenzyme A (CoA):Acetate CoA-Transferase Reveal Specificity Determinants and Illustrate the Mechanism Used by Class I CoA-Transferases journal October 2012
Specificity in Transition State Binding: The Pauling Model Revisited journal February 2013
Theoretical assessments of the basicity and nucleophilicity of carboxylate syn and anti lone pairs journal June 1989
Geometrical reaction coordinates. II. Nucleophilic addition to a carbonyl group journal July 1973
On Catalytic Preorganization in Oxyanion Holes: Highlighting the Problems with the Gas-Phase Modeling of Oxyanion Holes and Illustrating the Need for Complete Enzyme Models journal October 2010
Computational Study of the Citrate Synthase Catalyzed Deprotonation of Acetyl-Coenzyme A and Fluoroacetyl-Coenzyme A:  Demonstration of a Layered Quantum Mechanical Approach journal June 2003
Addgene provides an open forum for plasmid sharing journal April 2012
Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli journal June 2009
Announcing the worldwide Protein Data Bank journal December 2003
Cloning and Characterization of a Eukaryotic Pantothenate Kinase Gene ( panK ) from Aspergillus nidulans journal January 1999
The Antibiotic Activity of N -Pentylpantothenamide Results from Its Conversion to Ethyldethia-Coenzyme A, a Coenzyme A Antimetabolite journal October 2002
Iso-coenzyme A journal February 2005
Crystallographic refinement of ligand complexes journal December 2006
Features and development of Coot journal March 2010
A Specialized Citric Acid Cycle Requiring Succinyl-Coenzyme A (CoA):Acetate CoA-Transferase (AarC) Confers Acetic Acid Resistance on the Acidophile Acetobacter aceti journal May 2008
Degradation of Alkyl Methyl Ketones by Pseudomonas veronii MEK700 journal March 2007
Acylation of Biomolecules in Prokaryotes: a Widespread Strategy for the Control of Biological Function and Metabolic Stress journal July 2015
MOLE 2.0: advanced approach for analysis of biomacromolecular channels journal August 2013
X-Ray Diffraction data from succinyl-CoA:acetate CoA-transferase (EC 2.8.3.18), N347A mutant bound to CoA, source of 5DDK structure dataset May 2016
X-Ray Diffraction data from succinyl-CoA:acetate CoA-transferase (EC , source of 5DW4 structure dataset May 2016
X-Ray Diffraction data from succinyl-CoA:acetate CoA-transferase (EC 2.8.3.18), source of 5DW5 structure dataset July 2015
X-Ray Diffraction data from succinyl-CoA:acetate CoA-transferase (EC 2.8.3.18), source of 5DW6 structure dataset May 2016
X-Ray Diffraction data from succinyl-CoA:acetate CoA-transferase (EC 2.8.3.18), source of 5E5H structure dataset May 2016
PHENIX: a comprehensive Python-based system for macromolecular structure solution. text January 2010
The internal pH of Acetobacterium wieringae and Acetobacter aceti during growth and production of acetic acid journal October 1985
Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen journal August 2020
Mechanism and specificity of succinyl-CoA:3-ketoacid coenzyme A transferase. journal March 1976
Formation of active site thiol esters of CoA transferase and the dependence of catalysis on specific binding interactions. journal September 1982
Skeletal Muscle Coenzyme A Transferase journal February 1969
Identification of an Enzyme-γ-Glutamyl Coenzyme A Intermediate from Coenzyme A Transferase journal February 1969
Two functional domains of coenzyme A activate catalysis by coenzyme A transferase. Pantetheine and adenosine 3‘-phosphate 5‘-diphosphate. journal June 1986
[20] Processing of X-ray diffraction data collected in oscillation mode book January 1997
Protein production by auto-induction in high-density shaking cultures journal May 2005
Generation and stability of a simple thiol ester enolate in aqueous solution journal December 1992
PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome journal December 2019
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation journal February 2021
The Antibiotic Activity of N -Pentylpantothenamide Results from Its Conversion to Ethyldethia-Coenzyme A, a Coenzyme A Antimetabolite journal October 2002
Iso-coenzyme A journal February 2005
Mounting of crystals for macromolecular crystallography in a free-standing thin film journal October 1990
Crystallographic refinement of ligand complexes journal December 2006
MolProbity : all-atom structure validation for macromolecular crystallography journal December 2009
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
Features and development of Coot journal March 2010
To B or not to B : a question of resolution? journal March 2012
A Specialized Citric Acid Cycle Requiring Succinyl-Coenzyme A (CoA):Acetate CoA-Transferase (AarC) Confers Acetic Acid Resistance on the Acidophile Acetobacter aceti journal May 2008
Degradation of Alkyl Methyl Ketones by Pseudomonas veronii MEK700 journal March 2007
Acylation of Biomolecules in Prokaryotes: a Widespread Strategy for the Control of Biological Function and Metabolic Stress journal July 2015
An optimized growth medium for increased recombinant protein secretion titer via the type III secretion system journal February 2021

Similar Records

Structural snapshots along the reaction pathway of Yersinia pestis RipA, a putative butyryl-CoA transferase
Journal Article · Tue Apr 01 00:00:00 EDT 2014 · Acta Crystallographica. Section D: Biological Crystallography · OSTI ID:22351314
Crystallographic trapping of the glutamyl-CoA thioester intermediate of family I CoA transferases
Journal Article · Fri Dec 31 23:00:00 EST 2004 · J. Biol. Chem. · OSTI ID:913922
New spectrophotometric and radiochemical assays for acetyl-CoA: arylamine N-acetyltransferase applicable to a variety of arylamines
Journal Article · Thu Feb 28 23:00:00 EST 1985 · Anal. Biochem.; (United States) · OSTI ID:5253617

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES
enzyme mechanism
oxyanion hole
substrate analog
substrate-assisted catalysis