Structure of dimerized assimilatory NADPH-dependent sulfite reductase reveals the minimal interface for diflavin reductase binding
Abstract Escherichia coli NADPH-dependent assimilatory sulfite reductase (SiR) reduces sulfite by six electrons to make sulfide for incorporation into sulfur-containing biomolecules. SiR has two subunits: an NADPH, FMN, and FAD-binding diflavin flavoprotein and a siroheme/Fe4S4 cluster-containing he...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-03-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-58037-5 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850208501286043648 |
|---|---|
| author | Behrouz Ghazi Esfahani Nidhi Walia Kasahun Neselu Yashika Garg Mahira Aragon Isabel Askenasy Hui Alex Wei Joshua H. Mendez M. Elizabeth Stroupe |
| author_facet | Behrouz Ghazi Esfahani Nidhi Walia Kasahun Neselu Yashika Garg Mahira Aragon Isabel Askenasy Hui Alex Wei Joshua H. Mendez M. Elizabeth Stroupe |
| author_sort | Behrouz Ghazi Esfahani |
| collection | DOAJ |
| description | Abstract Escherichia coli NADPH-dependent assimilatory sulfite reductase (SiR) reduces sulfite by six electrons to make sulfide for incorporation into sulfur-containing biomolecules. SiR has two subunits: an NADPH, FMN, and FAD-binding diflavin flavoprotein and a siroheme/Fe4S4 cluster-containing hemoprotein. The molecular interactions that govern subunit binding have been unknown since the discovery of SiR over 50 years ago because SiR is flexible, thus has been intransigent for traditional high-resolution structural analysis. We use a combination of the chameleon® plunging system with a fluorinated lipid to overcome the challenges of preserving a flexible molecule to determine a 2.78 Å-resolution cryo-EM structure of a minimal heterodimer complex. Chameleon®, combined with the fluorinated lipid, overcomes persistent denaturation at the air-water interface. Using a previously characterized minimal heterodimer reduces the heterogeneity of a structurally heterogeneous complex to a level that we analyze using multi-conformer cryo-EM image analysis algorithms. Here, we report the near-atomic resolution structure of the flavoprotein/hemoprotein complex, revealing how they interact in a minimal interface. Further, we determine the structural elements that discriminate between pairing a hemoprotein with a diflavin reductase, as in the E. coli homolog, or a ferredoxin partner, as in maize (Zea mays). |
| format | Article |
| id | doaj-art-be9e034d54794a569b56dba7e1e69014 |
| institution | OA Journals |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-be9e034d54794a569b56dba7e1e690142025-08-20T02:10:13ZengNature PortfolioNature Communications2041-17232025-03-0116111210.1038/s41467-025-58037-5Structure of dimerized assimilatory NADPH-dependent sulfite reductase reveals the minimal interface for diflavin reductase bindingBehrouz Ghazi Esfahani0Nidhi Walia1Kasahun Neselu2Yashika Garg3Mahira Aragon4Isabel Askenasy5Hui Alex Wei6Joshua H. Mendez7M. Elizabeth Stroupe8Department of Biological Science and Institute of Molecular Biophysics, Florida State UniversityDepartment of Biological Science and Institute of Molecular Biophysics, Florida State UniversityNew York Structural Biology CenterDepartment of Biological Science and Institute of Molecular Biophysics, Florida State UniversityNew York Structural Biology CenterDepartment of Biological Science and Institute of Molecular Biophysics, Florida State UniversityNew York Structural Biology CenterNew York Structural Biology CenterDepartment of Biological Science and Institute of Molecular Biophysics, Florida State UniversityAbstract Escherichia coli NADPH-dependent assimilatory sulfite reductase (SiR) reduces sulfite by six electrons to make sulfide for incorporation into sulfur-containing biomolecules. SiR has two subunits: an NADPH, FMN, and FAD-binding diflavin flavoprotein and a siroheme/Fe4S4 cluster-containing hemoprotein. The molecular interactions that govern subunit binding have been unknown since the discovery of SiR over 50 years ago because SiR is flexible, thus has been intransigent for traditional high-resolution structural analysis. We use a combination of the chameleon® plunging system with a fluorinated lipid to overcome the challenges of preserving a flexible molecule to determine a 2.78 Å-resolution cryo-EM structure of a minimal heterodimer complex. Chameleon®, combined with the fluorinated lipid, overcomes persistent denaturation at the air-water interface. Using a previously characterized minimal heterodimer reduces the heterogeneity of a structurally heterogeneous complex to a level that we analyze using multi-conformer cryo-EM image analysis algorithms. Here, we report the near-atomic resolution structure of the flavoprotein/hemoprotein complex, revealing how they interact in a minimal interface. Further, we determine the structural elements that discriminate between pairing a hemoprotein with a diflavin reductase, as in the E. coli homolog, or a ferredoxin partner, as in maize (Zea mays).https://doi.org/10.1038/s41467-025-58037-5 |
| spellingShingle | Behrouz Ghazi Esfahani Nidhi Walia Kasahun Neselu Yashika Garg Mahira Aragon Isabel Askenasy Hui Alex Wei Joshua H. Mendez M. Elizabeth Stroupe Structure of dimerized assimilatory NADPH-dependent sulfite reductase reveals the minimal interface for diflavin reductase binding Nature Communications |
| title | Structure of dimerized assimilatory NADPH-dependent sulfite reductase reveals the minimal interface for diflavin reductase binding |
| title_full | Structure of dimerized assimilatory NADPH-dependent sulfite reductase reveals the minimal interface for diflavin reductase binding |
| title_fullStr | Structure of dimerized assimilatory NADPH-dependent sulfite reductase reveals the minimal interface for diflavin reductase binding |
| title_full_unstemmed | Structure of dimerized assimilatory NADPH-dependent sulfite reductase reveals the minimal interface for diflavin reductase binding |
| title_short | Structure of dimerized assimilatory NADPH-dependent sulfite reductase reveals the minimal interface for diflavin reductase binding |
| title_sort | structure of dimerized assimilatory nadph dependent sulfite reductase reveals the minimal interface for diflavin reductase binding |
| url | https://doi.org/10.1038/s41467-025-58037-5 |
| work_keys_str_mv | AT behrouzghaziesfahani structureofdimerizedassimilatorynadphdependentsulfitereductaserevealstheminimalinterfacefordiflavinreductasebinding AT nidhiwalia structureofdimerizedassimilatorynadphdependentsulfitereductaserevealstheminimalinterfacefordiflavinreductasebinding AT kasahunneselu structureofdimerizedassimilatorynadphdependentsulfitereductaserevealstheminimalinterfacefordiflavinreductasebinding AT yashikagarg structureofdimerizedassimilatorynadphdependentsulfitereductaserevealstheminimalinterfacefordiflavinreductasebinding AT mahiraaragon structureofdimerizedassimilatorynadphdependentsulfitereductaserevealstheminimalinterfacefordiflavinreductasebinding AT isabelaskenasy structureofdimerizedassimilatorynadphdependentsulfitereductaserevealstheminimalinterfacefordiflavinreductasebinding AT huialexwei structureofdimerizedassimilatorynadphdependentsulfitereductaserevealstheminimalinterfacefordiflavinreductasebinding AT joshuahmendez structureofdimerizedassimilatorynadphdependentsulfitereductaserevealstheminimalinterfacefordiflavinreductasebinding AT melizabethstroupe structureofdimerizedassimilatorynadphdependentsulfitereductaserevealstheminimalinterfacefordiflavinreductasebinding |