Statistical analyses of the oxidized P-clusters in MoFe proteins using the bond-valence method: towards their electron transfer in nitrogenases

• Published in: Acta crystallographica. Section D, Biological crystallography. Vol. 79; no. Pt 5; pp. 401 - 408
• Main Authors: Xie, Zhen Lang, Yuan, Chang, Zhou, Zhao Hui
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 01.05.2023
• Subjects: Atomic properties; Azotobacter vinelandii - chemistry; Azotobacter vinelandii - metabolism; Clusters; Crystallography; Electron Spin Resonance Spectroscopy; Electron transfer; Electron Transport; Electrons; Molybdoferredoxin - chemistry; Nitrogenase - chemistry; Oxidation; Oxidation-Reduction; Proteins; Protonation; Statistical analysis; oxidation states; double protonation; MoFe proteins; oxidized P-clusters; bond-valence method
• ISSN: 0907-4449; 2059-7983; 1399-0047
• DOI: 10.1107/S2059798323002474

26 well selected oxidized P-clusters (P ) from the crystallographic data deposited in the Protein Data Bank have been analysed statistically by the bond-valence sum method with weighting schemes for MoFe proteins at different resolutions. Interestingly, the oxidation states of P clusters correspond to Fe Fe with high electron delocalization, showing the same oxidation states as the resting states of P-clusters (P ) in nitrogenases. The previously uncertain reduction of P to P clusters by two electrons was assigned as a double protonation of P , in which decoordination of the serine residue and the peptide chain of cysteine take place, in MoFe proteins. This is further supported by the obviously shorter α-alkoxy C-O bond (average of 1.398 Å) in P clusters and longer α-hydroxy C-O bond (average of 1.422 Å) in P clusters, while no change is observed in the electronic structures of Fe S Fe atoms in P-clusters. Spatially, the calculations show that Fe3 and Fe6, the most oxidized and most reduced Fe atoms, have the shortest distances of 9.329 Å from the homocitrate in the FeMo cofactor and 14.947 Å from the [Fe S ] cluster, respectively, and may well function as important electron-transport sites.