Publication:
Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus

dc.contributor.coauthorTolar, Bradley B.
dc.contributor.coauthorYoshikuni, Yasuo
dc.contributor.coauthorFrancis, Christopher A.
dc.contributor.coauthorWakatsuki, Soichi
dc.contributor.departmentDepartment of Molecular Biology and Genetics
dc.contributor.departmentGraduate School of Sciences and Engineering
dc.contributor.kuauthorDemirci, Hasan
dc.contributor.kuauthorJohnson, Jerome Austin
dc.contributor.kuauthorTosun, Bilge
dc.contributor.schoolcollegeinstituteCollege of Sciences
dc.contributor.schoolcollegeinstituteGRADUATE SCHOOL OF SCIENCES AND ENGINEERING
dc.date.accessioned2025-03-06T20:57:50Z
dc.date.issued2024
dc.description.abstractThe 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.indexedbyWOS
dc.description.indexedbyScopus
dc.description.indexedbyPubMed
dc.description.publisherscopeInternational
dc.description.sponsoredbyTubitakEuTÜBİTAK
dc.description.sponsorshipThis 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.doi10.1038/s42003-024-06432-x
dc.identifier.eissn2399-3642
dc.identifier.grantnoTÜBİTAK-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.issue1
dc.identifier.quartileQ1
dc.identifier.scopus2-s2.0-85206970852
dc.identifier.urihttps://doi.org/10.1038/s42003-024-06432-x
dc.identifier.urihttps://hdl.handle.net/20.500.14288/27325
dc.identifier.volume7
dc.identifier.wos1337764200003
dc.keywords3-hydroxypropionate/4-hydroxybutyrate cycle
dc.keywordsThaumarchaeota
dc.keywordsNitrosopumilus maritimus
dc.keywords4-hydroxybutyryl-CoA synthetase
dc.keywordsEnergy-efficient carbon fixation
dc.keywordsCoA-binding domain
dc.keywordsATP-grasp domain
dc.keywordsPhylogenetic analysis
dc.keywordsAcyl-CoA synthetase superfamily
dc.keywordsStructural stability
dc.keywordsOligomer stability
dc.language.isoeng
dc.publisherNature Portfolio
dc.relation.ispartofCOMMUNICATIONS BIOLOGY
dc.subjectBiology
dc.subjectMultidisciplinary sciences
dc.titleCrystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus
dc.typeJournal Article
dspace.entity.typePublication
local.contributor.kuauthorDemirci, Hasan
local.contributor.kuauthorTosun, Bilge
local.contributor.kuauthorJohnson, Jerome Austin
local.publication.orgunit1College of Sciences
local.publication.orgunit1GRADUATE SCHOOL OF SCIENCES AND ENGINEERING
local.publication.orgunit2Department of Molecular Biology and Genetics
local.publication.orgunit2Graduate School of Sciences and Engineering
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