Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus
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...
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2024-10-01
|
| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-024-06432-x |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850201912458084352 |
|---|---|
| author | Jerome Johnson Bradley B. Tolar Bilge Tosun Yasuo Yoshikuni Christopher A. Francis Soichi Wakatsuki Hasan DeMirci |
| author_facet | Jerome Johnson Bradley B. Tolar Bilge Tosun Yasuo Yoshikuni Christopher A. Francis Soichi Wakatsuki Hasan DeMirci |
| author_sort | Jerome Johnson |
| collection | DOAJ |
| 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. |
| format | Article |
| id | doaj-art-b0074faf961d4e1784f937a5b876db42 |
| institution | OA Journals |
| issn | 2399-3642 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj-art-b0074faf961d4e1784f937a5b876db422025-08-20T02:11:54ZengNature PortfolioCommunications Biology2399-36422024-10-017111010.1038/s42003-024-06432-xCrystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimusJerome Johnson0Bradley B. Tolar1Bilge Tosun2Yasuo Yoshikuni3Christopher A. Francis4Soichi Wakatsuki5Hasan DeMirci6Department of Molecular Biology and Genetics, Koç UniversityDepartment of Earth System Science, Stanford UniversityDepartment of Molecular Biology and Genetics, Koç UniversityThe US DOE Joint Genome Institute, Lawrence Berkeley National LaboratoryDepartment of Earth System Science, Stanford UniversityDepartment of Structural Biology, Stanford UniversityDepartment of Molecular Biology and Genetics, Koç UniversityAbstract 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.https://doi.org/10.1038/s42003-024-06432-x |
| spellingShingle | Jerome Johnson Bradley B. Tolar Bilge Tosun Yasuo Yoshikuni Christopher A. Francis Soichi Wakatsuki Hasan DeMirci Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus Communications Biology |
| title | Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus |
| title_full | Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus |
| title_fullStr | Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus |
| title_full_unstemmed | Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus |
| title_short | Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus |
| title_sort | crystal structure of the 4 hydroxybutyryl coa synthetase adp forming from nitrosopumilus maritimus |
| url | https://doi.org/10.1038/s42003-024-06432-x |
| work_keys_str_mv | AT jeromejohnson crystalstructureofthe4hydroxybutyrylcoasynthetaseadpformingfromnitrosopumilusmaritimus AT bradleybtolar crystalstructureofthe4hydroxybutyrylcoasynthetaseadpformingfromnitrosopumilusmaritimus AT bilgetosun crystalstructureofthe4hydroxybutyrylcoasynthetaseadpformingfromnitrosopumilusmaritimus AT yasuoyoshikuni crystalstructureofthe4hydroxybutyrylcoasynthetaseadpformingfromnitrosopumilusmaritimus AT christopherafrancis crystalstructureofthe4hydroxybutyrylcoasynthetaseadpformingfromnitrosopumilusmaritimus AT soichiwakatsuki crystalstructureofthe4hydroxybutyrylcoasynthetaseadpformingfromnitrosopumilusmaritimus AT hasandemirci crystalstructureofthe4hydroxybutyrylcoasynthetaseadpformingfromnitrosopumilusmaritimus |