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Revealing reaction intermediates in one-carbon elongation by thiamine diphosphate/CoA-dependent enzyme family

Journal Article · · Communications Chemistry
 [1];  [2];  [3];  [4];  [3];  [5];  [2];  [4];  [2];  [4];  [6];  [7];  [2];  [1];  [1]
  1. Argonne National Laboratory (ANL), Argonne, IL (United States); University of Chicago, IL (United States)
  2. University of South Florida, Tampa, FL (United States)
  3. University of Chicago, IL (United States)
  4. Max Planck Institute for Terrestrial Microbiology, Marburg (Germany)
  5. Argonne National Laboratory (ANL), Argonne, IL (United States)
  6. Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
  7. Max Planck Institute for Terrestrial Microbiology, Marburg (Germany); Center for Synthetic Microbiology (SYNMIKRO), Marburg (Germany)
+ Show Author Affiliations
2-Hydroxyacyl-CoA lyase/synthase (HACL/S) is a thiamine diphosphate (ThDP)-dependent versatile enzyme originally discovered in the mammalian α-oxidation pathway. HACL/S natively cleaves 2-hydroxyacyl-CoAs and, in its reverse direction, condenses formyl-CoA with aldehydes or ketones. The one-carbon elongation biochemistry based on HACL/S has enabled the use of molecules derived from greenhouse gases as biomanufacturing feedstocks. We investigated several HACL/S family members with high activity in the condensation of formyl-CoA and aldehydes, and distinct chain-length specificities and kinetic parameters. Our analysis revealed the structures of enzymes in complex with acyl-CoA substrates and products, several covalent intermediates, bound ThDP and ADP, as well as the C-terminal active site region. One of these observed states corresponds to the intermediary α–carbanion with hydroxymethyl-CoA covalently attached to ThDP. This research distinguishes HACL/S from related sub-families and identifies key residues involved in substrate binding and catalysis. These findings expand our knowledge of acyloin-condensation biochemistry and offer attractive prospects for biocatalysis using carbon elongation.
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Montana State University, Bozeman, MT (United States)
Sponsoring Organization:
USDOE Joint Genome Institute (JGI); USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-05CH11231; AC02-06CH11357; EE0008499
OSTI ID:
2478674
Alternate ID(s):
OSTI ID: 2440637
Journal Information:
Communications Chemistry, Journal Name: Communications Chemistry Journal Issue: 1 Vol. 7; ISSN 2399-3669
Publisher:
Springer NatureCopyright Statement
Country of Publication:
United States
Language:
English

References (29)

Oxalyl‐CoA Decarboxylase Enables Nucleophilic One‐Carbon Extension of Aldehydes to Chiral α‐Hydroxy Acids journal February 2020
Development of a kinetic model and figures of merit for formaldehyde carboligations catalyzed by formolase enzymes journal September 2022
Protein Production for Structural Genomics Using E. coli Expression book January 2014
Structure, mechanism and catalytic duality of thiamine-dependent enzymes journal February 2007
Formate Metabolism journal August 1963
Mechanistic details of the actinobacterial lyase-catalyzed degradation reaction of 2-hydroxyisobutyryl-CoA journal January 2022
Frontiers in the enzymology of thiamin diphosphate-dependent enzymes journal October 2022
Crystallographic Snapshots of Oxalyl-CoA Decarboxylase Give Insights into Catalysis by Nonoxidative ThDP-Dependent Decarboxylases journal July 2007
Automated data collection for macromolecular crystallography journal September 2011
Engineering a Highly Efficient Carboligase for Synthetic One-Carbon Metabolism journal April 2021
Identification of 2-Hydroxyacyl-CoA Synthases with High Acyloin Condensation Activity for Orthogonal One-Carbon Bioconversion journal August 2023
Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo journal May 2023
Highly accurate protein structure prediction with AlphaFold journal July 2021
2-Hydroxyacyl-CoA lyase catalyzes acyloin condensation for one-carbon bioconversion journal August 2019
A new-to-nature carboxylation module to improve natural and synthetic CO2 fixation journal January 2021
An orthogonal metabolic framework for one-carbon utilization journal October 2021
Unexpected tautomeric equilibria of the carbanion-enamine intermediate in pyruvate oxidase highlight unrecognized chemical versatility of thiamin journal June 2012
Purification, molecular cloning, and expression of 2-hydroxyphytanoyl-CoA lyase, a peroxisomal thiamine pyrophosphate-dependent enzyme that catalyzes the carbon–carbon bond cleavage during α-oxidation of 3-methyl-branched fatty acids journal August 1999
Kinetic and Mechanistic Characterization of the Formyl-CoA Transferase from Oxalobacter formigenes journal August 2004
Structural Basis for Activation of the Thiamin Diphosphate-dependent Enzyme Oxalyl-CoA Decarboxylase by Adenosine Diphosphate* journal December 2005
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes journal July 2004
PROCHECK: a program to check the stereochemical quality of protein structures journal April 1993
MOLREP an Automated Program for Molecular Replacement journal December 1997
Coot model-building tools for molecular graphics journal November 2004
HKL -3000: the integration of data reduction and structure solution – from diffraction images to an initial model in minutes journal July 2006
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
REFMAC 5 for the refinement of macromolecular crystal structures journal March 2011
Linking Crystallographic Model and Data Quality journal May 2012
A Chemo-Enzymatic Road Map to the Synthesis of CoA Esters journal April 2016

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Related Subjects

2-hydroxyacyl-CoA lyase
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
X-ray crystallography
biocatalysis
catalytic mechanism
condensation aldehydes and ketones
crystal structure
enzyme mechanisms
synthase
thiamine diphosphate-dependent