Evidence map›Paper›PMID 39034323›Full record

ArticleCommunications chemistry2024

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

Youngchang Kim, Seung Hwan Lee, Priyanka Gade, Maren Nattermann, Natalia Maltseva, Michael Endres, Jing Chen, Philipp Wichmann, Yang Hu, Daniel G Marchal and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Communications chemistry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Youngchang KimeBERlight and Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA.
Seung Hwan LeeDepartment of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA.
Priyanka GadeConsortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.
Maren NattermannDepartment of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Natalia MaltsevaConsortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0002-2871-465X
Michael EndreseBERlight and Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA.
Jing ChenDepartment of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA.
Philipp WichmannDepartment of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.ORCID http://orcid.org/0000-0003-2620-360X
Yang HuDepartment of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA.
Daniel G MarchalDepartment of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.ORCID http://orcid.org/0009-0002-1314-4583
Yasuo YoshikuniThe US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. yyoshikuni@lbl.gov.ORCID http://orcid.org/0000-0002-8372-640X
Tobias J ErbDepartment of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.ORCID http://orcid.org/0000-0003-3685-0894
Ramon GonzalezDepartment of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA. ramongonzale@usf.edu.ORCID http://orcid.org/0000-0003-4797-6580
Karolina MichalskaeBERlight and Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA. kmichalska@anl.gov.ORCID http://orcid.org/0000-0001-7140-3649
Andrzej JoachimiakeBERlight and Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA. andrzejj@anl.gov.ORCID http://orcid.org/0000-0003-2535-6209

Funding

U.S. Department of Energy (DOE) DE-AC02-05CH11231U.S. Department of Energy (DOE) DE-AC02-06CH11357U.S. Department of Energy (DOE) DE-EE0008499
6 · The paper itself

Abstract

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.

Identifiers

PMID39034323
PMCPMC11271303

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.