The crystal structure of Shethna protein II (FeSII) from Azotobacter vinelandii suggests a domain swap
OA Location
Author(s)
Type
Journal Article
Abstract
The Azotobacter vinelandii FeSII protein forms an oxygen-resistant complex with the nitrogenase MoFe and Fe proteins. FeSII is an adrenodoxin-type ferredoxin that forms a dimer in solution. Previously, the crystal structure was solved [Schlesier et al. (2016), J. Am. Chem. Soc. 138, 239–247] with five copies in the asymmetric unit. One copy is a normal adrenodoxin domain that forms a dimer with its crystallographic symmetry mate. The other four copies are in an `open' conformation with a loop flipped out exposing the 2Fe–2S cluster. The open and closed conformations were interpreted as oxidized and reduced, respectively, and the large conformational change in the open configuration allowed binding to nitrogenase. Here, the structure of FeSII was independently solved in the same crystal form. The positioning of the atoms in the unit cell is similar to the earlier report. However, the interpretation of the structure is different. The `open' conformation is interpreted as the product of a crystallization-induced domain swap. The 2Fe–2S cluster is not exposed to solvent, but in the crystal its interacting helix is replaced by the same helix residues from a crystal symmetry mate. The domain swap is complicated, as it is unusual in being in the middle of the protein rather than at a terminus, and it creates arrangements of molecules that can be interpreted in multiple ways. It is also cautioned that crystal structures should be interpreted in terms of the contents of the entire crystal rather than of one asymmetric unit.
Date Issued
2024-08-01
Date Acceptance
2024-06-18
Citation
Acta Crystallographica Section D: Structural Biology, 2024, 80 (Part 8), pp.599-604
ISSN
2059-7983
Publisher
International Union of Crystallography
Start Page
599
End Page
604
Journal / Book Title
Acta Crystallographica Section D: Structural Biology
Volume
80
Issue
Part 8
Copyright Statement
© 2024 The Author(s). Published under a CC BY 4.0 licence
License URL
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/38984904
PII: S2059798324005928
Subjects
2FE-2S FERREDOXIN
Azotobacter vinelandii
BINDING PROTEIN
Biochemical Research Methods
Biochemistry & Molecular Biology
Biophysics
CONFORMATIONAL PROTECTION
Crystallography
domain swapping
FeSII protein
Life Sciences & Biomedicine
nitrogen fixation
NITROGEN-FIXATION
OXYGEN
oxygen protection
Physical Sciences
RHODOBACTER-CAPSULATUS
Science & Technology
Shethna protein II
structural biology
Publication Status
Published
Coverage Spatial
United States
Date Publish Online
2024-07-10