Title: Four amino acids define the CO ₂ binding pocket of enoyl-CoA carboxylases/reductases

Abstract

Carboxylases are biocatalysts that capture and convert carbon dioxide (CO₂) under mild conditions and atmospheric concentrations at a scale of more than 400 Gt annually. However, how these enzymes bind and control the gaseous CO₂molecule during catalysis is only poorly understood. One of the most efficient classes of carboxylating enzymes are enoyl-CoA carboxylases/reductases (Ecrs), which outcompete the plant enzyme RuBisCO in catalytic efficiency and fidelity by more than an order of magnitude. Here we investigated the interactions of CO₂within the active site of Ecr fromKitasatospora setae. Combining experimental biochemistry, protein crystallography, and advanced computer simulations we show that 4 amino acids, N81, F170, E171, and H365, are required to create a highly efficient CO₂-fixing enzyme. Together, these 4 residues anchor and position the CO₂molecule for the attack by a reactive enolate created during the catalytic cycle. Notably, a highly ordered water molecule plays an important role in an active site that is otherwise carefully shielded from water, which is detrimental to CO₂fixation. Altogether, our study reveals unprecedented molecular details of selective CO₂binding and C–C-bond formation during the catalytic cycle of nature’s most efficient CO₂-fixing enzyme. This knowledge provides the basis for the future development of catalytic frameworks for the capturemore » and conversion of CO₂in biology and chemistry.« less

Authors:

Stoffel, Gabriele M. M. ^[1]; Saez, David Adrian  ^[2];

• Search DOE PAGES for author "Saez, David Adrian"
• Search DOE PAGES for ORCID "0000-0001-5555-8720"

DeMirci, Hasan ^[3]; Vögeli, Bastian ^[4]; Rao, Yashas ^[5]; Zarzycki, Jan  ^[1];

• Search DOE PAGES for author "Zarzycki, Jan"
• Search DOE PAGES for ORCID "0000-0002-6307-6497"

Yoshikuni, Yasuo  ^[6];

• Search DOE PAGES for author "Yoshikuni, Yasuo"
• Search DOE PAGES for ORCID "0000-0002-8372-640X"

Wakatsuki, Soichi  ^[7];

• Search DOE PAGES for author "Wakatsuki, Soichi"
• Search DOE PAGES for ORCID "0000-0001-5896-7968"

Vöhringer-Martinez, Esteban ^[2]; Erb, Tobias J. ^[1]

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+ Show Author Affiliations

1. Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany,, Center for Synthetic Microbiology, D-35043 Marburg, Germany,
2. Departamento de Físico Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070371 Concepción, Chile,
3. Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,, Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
4. Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany,
5. Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,
6. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598,
7. Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025,, Structural Biology Department, Stanford University, Stanford, CA 94305

Publication Date:

Wed Jun 26 00:00:00 EDT 2019

Research Org.:

SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:

1529676

Alternate Identifier(s):

OSTI ID: 1546799; OSTI ID: 1559229

Grant/Contract Number:  

AC02-05CH11231; AC02-76SF00515; 637675; 1231306

Resource Type:

Published Article

Journal Name:

Proceedings of the National Academy of Sciences of the United States of America

Additional Journal Information:

Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Volume: 116 Journal Issue: 28; Journal ID: ISSN 0027-8424

Publisher:

Proceedings of the National Academy of Sciences

Country of Publication:

United States

Language:

English

Subject:

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY