Publication: Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus
dc.contributor.coauthor | Tolar, Bradley B. | |
dc.contributor.coauthor | Yoshikuni, Yasuo | |
dc.contributor.coauthor | Francis, Christopher A. | |
dc.contributor.coauthor | Wakatsuki, Soichi | |
dc.contributor.department | Department of Molecular Biology and Genetics | |
dc.contributor.department | Graduate School of Sciences and Engineering | |
dc.contributor.kuauthor | Demirci, Hasan | |
dc.contributor.kuauthor | Johnson, Jerome Austin | |
dc.contributor.kuauthor | Tosun, Bilge | |
dc.contributor.schoolcollegeinstitute | College of Sciences | |
dc.contributor.schoolcollegeinstitute | GRADUATE SCHOOL OF SCIENCES AND ENGINEERING | |
dc.date.accessioned | 2025-03-06T20:57:50Z | |
dc.date.issued | 2024 | |
dc.description.abstract | The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle from ammonia-oxidizing Thaumarchaeota is currently considered the most energy-efficient aerobic carbon fixation pathway. The Nitrosopumilus maritimus 4-hydroxybutyryl-CoA synthetase (ADP-forming;Nmar_0206) represents one of several enzymes from this cycle that exhibit increased efficiency over crenarchaeal counterparts. This enzyme reduces energy requirements on the cell, reflecting thaumarchaeal success in adapting to low-nutrient environments. Here we show the structure of Nmar_0206 from Nitrosopumilus maritimus SCM1, which reveals a highly conserved interdomain linker loop between the CoA-binding and ATP-grasp domains. Phylogenetic analysis suggests the widespread prevalence of this loop and highlights both its underrepresentation within the PDB and structural importance within the (ATP-forming) acyl-CoA synthetase (ACD) superfamily. This linker is shown to have a possible influence on conserved interface interactions between domains, thereby influencing homodimer stability. These results provide a structural basis for the energy efficiency of this key enzyme in the modified 3HP/4HB cycle of Thaumarchaeota. Structural analysis suggests the importance of linkers in stability of oligomers within the (ADP-forming) Acyl-CoA Synthetase superfamily. | |
dc.description.indexedby | WOS | |
dc.description.indexedby | Scopus | |
dc.description.indexedby | PubMed | |
dc.description.publisherscope | International | |
dc.description.sponsoredbyTubitakEu | TÜBİTAK | |
dc.description.sponsorship | This project and the experiments are funded by TÜBİTAK-NSF 2501 bilateral research program (project number 221N355). H.D. acknowledges support from NSF Science and Technology Center grant NSF-1231306 (Biology with X-ray Lasers, BioXFEL). This publication has been produced benefiting from the 2232 International Fellowship for Outstanding Researchers Program and the 1001 Scientific and Technological Research Projects Funding Program of the TÜBİTAK (Project Nos. 118C270 and 120Z520). However, the entire responsibility of the publication belongs to the authors of the publication. The financial support received from TÜBİTAK does not mean that the content of the publication is approved in a scientific sense by TÜBİTAK. The work conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. SW and CAF acknowledge support from the U.S. Department of Energy (DOE) Office of Science, Biological and Environmental Research;Stanford Precourt Institute;and SLAC Laboratory Directed Research and Development. SSRL is supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences (OBES) under Contract No. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research and by the National Institutes of Health, National Institute of General Medical Sciences (NIGMS) (including P41GM103393).https://docs.google.com/document/d/15DKqmvS4hWirc7UkWO6nGVCpnu6zwXQnF-opz30YEp0/edit. | |
dc.identifier.doi | 10.1038/s42003-024-06432-x | |
dc.identifier.eissn | 2399-3642 | |
dc.identifier.grantno | TÜBİTAK-NSF 2501 bilateral research program [221N355];NSF Science and Technology Center [NSF-1231306];TÜBİTAK [118C270, 120Z520];Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231];U.S. Department of Energy (DOE) Office of Science, Biological and Environmental Research;Stanford Precourt Institute;SLAC Laboratory Directed Research and Development;U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences (OBES) [DE-AC02-76SF00515];DOE Office of Biological and Environmental Research;National Institutes of Health, National Institute of General Medical Sciences (NIGMS) [P41GM103393] | |
dc.identifier.issue | 1 | |
dc.identifier.quartile | Q1 | |
dc.identifier.scopus | 2-s2.0-85206970852 | |
dc.identifier.uri | https://doi.org/10.1038/s42003-024-06432-x | |
dc.identifier.uri | https://hdl.handle.net/20.500.14288/27325 | |
dc.identifier.volume | 7 | |
dc.identifier.wos | 1337764200003 | |
dc.keywords | 3-hydroxypropionate/4-hydroxybutyrate cycle | |
dc.keywords | Thaumarchaeota | |
dc.keywords | Nitrosopumilus maritimus | |
dc.keywords | 4-hydroxybutyryl-CoA synthetase | |
dc.keywords | Energy-efficient carbon fixation | |
dc.keywords | CoA-binding domain | |
dc.keywords | ATP-grasp domain | |
dc.keywords | Phylogenetic analysis | |
dc.keywords | Acyl-CoA synthetase superfamily | |
dc.keywords | Structural stability | |
dc.keywords | Oligomer stability | |
dc.language.iso | eng | |
dc.publisher | Nature Portfolio | |
dc.relation.ispartof | COMMUNICATIONS BIOLOGY | |
dc.subject | Biology | |
dc.subject | Multidisciplinary sciences | |
dc.title | Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus | |
dc.type | Journal Article | |
dspace.entity.type | Publication | |
local.contributor.kuauthor | Demirci, Hasan | |
local.contributor.kuauthor | Tosun, Bilge | |
local.contributor.kuauthor | Johnson, Jerome Austin | |
local.publication.orgunit1 | College of Sciences | |
local.publication.orgunit1 | GRADUATE SCHOOL OF SCIENCES AND ENGINEERING | |
local.publication.orgunit2 | Department of Molecular Biology and Genetics | |
local.publication.orgunit2 | Graduate School of Sciences and Engineering | |
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