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Reconsideration of the P-clusters in VFe proteins using the bond-valence method: towards their electron transfer and protonation.
Acta Crystallographica Section D ( IF 2.6 ) Pub Date : 2025-02-01 , DOI: 10.1107/s2059798325000415
Zhen Lang Xie,Wan Ting Jin,Zhao Hui Zhou

P-clusters have been statistically analysed using the bond-valence sum (BVS) method together with weighting schemes. The crystallographic data come from the VFe proteins deposited in the Protein Data Bank (PDB) with high resolutions of better than 1.35 Å. Calculations show that the formal oxidation state of a P1+ cluster can be assigned as 2Fe3+6Fe2+ with high electron delocalization, giving the same oxidation state as that of PN clusters in VFe proteins. Further comprehensive comparisons of the bond distances suggest that the hydroxyl groups of the β-153 serine residues in P1+ and PN clusters are in the protonated state, where the Fe6 atoms have the same oxidation state as Fe2+. During the transition from PN to P1+, cleavage of the Fe6-S1 bond is accompanied by the formation of a weak coordination between the Fe6 atom and the hydroxyl group of the β-153 serine residue in the P1+ cluster of the VFe protein. Similarly, oxidation of PN to P1+/P2+ clusters corresponds to the coordination of Fe6(II) by the hydroxyl group of the β-188 serine residue and of Fe5(II) by the peptide amine group of the α-88 cysteine residue in the MoFe protein of Azotobacter vinelandiis without electron and proton transfers.

中文翻译:


使用键价法重新考虑 VFe 蛋白中的 P 簇:走向它们的电子转移和质子化。



已使用键价和 (BVS) 方法以及加权方案对 P 簇进行了统计分析。晶体学数据来自保存在蛋白质数据库 (PDB) 中的 VFe 蛋白,具有优于 1.35 Å 的高分辨率。计算表明,P1 + 簇的正式氧化态可以指定为具有高电子离域性的 2Fe3 + 6Fe2 + ,从而获得与 VFe 蛋白中 PN 簇相同的氧化态。键距的进一步综合比较表明,P1+ 和 PN 簇中 β-153 丝氨酸残基的羟基处于质子化状态,其中 Fe6 原子与 Fe2+ 具有相同的氧化态。在从 PN 到 P1+ 的转变过程中,Fe6-S1 键的裂解伴随着 Fe6 原子与 VFe 蛋白 P1+ 簇中 β-153 丝氨酸残基的羟基之间形成弱配位。同样,PN 氧化成 P1+/P2+ 簇对应于 β-188 丝氨酸残基的羟基对 Fe6(II) 的配位,以及 Azotobacter vinelandiis 的 MoFe 蛋白中 α-88 半胱氨酸残基的肽胺基对 Fe5(II) 的配位,没有电子和质子转移。
更新日期:2025-01-24
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