鉴定与来自大肠杆菌的细胞色素bo3的Q(H)位点处的半醌氢键合的氮供体。
Identification of the nitrogen donor hydrogen bonded with the semiquinone at the Q(H) site of the cytochrome bo3 from Escherichia coli.
作者信息
Lin Myat T, Samoilova Rimma I, Gennis Robert B, Dikanov Sergei A
机构信息
Department of Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
出版信息
J Am Chem Soc. 2008 Nov 26;130(47):15768-9. doi: 10.1021/ja805906a.
Abstract
The selective (15)N isotope labeling was used for the identification of the nitrogen involved in a hydrogen bond formation with the semiquinone in the high-affinity Q(H) site in the cytochrome bo(3) ubiquinol oxidase. This nitrogen produces dominating contribution to X-Band (14)N ESEEM spectra. The 2D ESEEM (HYSCORE) experiments with the Q(H) site SQ in the series of selectively (15)N labeled bo(3) oxidase proteins have directly identified the N(epsilon) of R71 as an H-bond donor. In addition, selective (15)N labeling has allowed us for the first time to determine weak hyperfine couplings with the side-chain nitrogens from all residues around the SQ. Those are reflecting a distribution of the unpaired spin density over the protein in the SQ state of the quinone processing site.
摘要
采用选择性（15）N同位素标记来鉴定与细胞色素bo（3）泛醇氧化酶高亲和力Q（H）位点中的半醌形成氢键的氮。该氮对X波段（14）N电子自旋回波包络调制（ESEEM）光谱有主要贡献。在一系列选择性（15）N标记的bo（3）氧化酶蛋白中，对Q（H）位点半醌进行二维ESEEM（高分辨二维电子自旋回波包络调制，HYSCORE）实验，直接确定R71的N（ε）作为氢键供体。此外，选择性（15）N标记首次使我们能够确定与半醌周围所有残基的侧链氮的弱超精细耦合。这些反映了醌处理位点处于半醌状态时蛋白质上未配对自旋密度的分布。
相似文献
1
Identification of the nitrogen donor hydrogen bonded with the semiquinone at the Q(H) site of the cytochrome bo3 from Escherichia coli.鉴定与来自大肠杆菌的细胞色素bo3的Q(H)位点处的半醌氢键合的氮供体。
J Am Chem Soc. 2008 Nov 26;130(47):15768-9. doi: 10.1021/ja805906a.
2
Interactions of intermediate semiquinone with surrounding protein residues at the Q(H) site of wild-type and D75H mutant cytochrome bo3 from Escherichia coli.野生型和 D75H 突变型大肠杆菌细胞色素 bo3 的 Q(H) 部位中间半醌与周围蛋白残基的相互作用。
Biochemistry. 2012 May 8;51(18):3827-38. doi: 10.1021/bi300151q. Epub 2012 Apr 22.
3
Plasticity in the High Affinity Menaquinone Binding Site of the Cytochrome aa3-600 Menaquinol Oxidase from Bacillus subtilis.枯草芽孢杆菌细胞色素aa3-600甲萘醌醇氧化酶高亲和力甲萘醌结合位点的可塑性
Biochemistry. 2015 Aug 18;54(32):5030-44. doi: 10.1021/acs.biochem.5b00528. Epub 2015 Aug 6.
4
Hydrogen bonds between nitrogen donors and the semiquinone in the Q(B) site of bacterial reaction centers.供体氮原子与细菌反应中心 Q(B)部位半醌之间的氢键。
J Am Chem Soc. 2010 Aug 25;132(33):11671-7. doi: 10.1021/ja104134e.
5
Probing molecular interactions of semiquinone radicals at quinone reduction sites of cytochrome by X-band HYSCORE EPR spectroscopy and quantum mechanical calculations.通过 X 波段 HYSCORE EPR 光谱和量子力学计算研究细胞色素中醌还原部位半醌自由基的分子相互作用。
Phys Chem Chem Phys. 2023 Aug 23;25(33):21935-21943. doi: 10.1039/d3cp02433d.
6
Two-Dimensional Pulsed EPR Resolves Hyperfine Coupling Strain in Nitrogen Hydrogen Bond Donors of Semiquinone Intermediates.二维脉冲电子顺磁共振解析半醌中间体中氮氢键给体的超精细耦合应变。
J Phys Chem B. 2018 May 24;122(20):5205-5211. doi: 10.1021/acs.jpcb.8b02511. Epub 2018 May 10.
7
Characterization of mutants that change the hydrogen bonding of the semiquinone radical at the QH site of the cytochrome bo3 from Escherichia coli.对改变大肠杆菌细胞色素bo3的QH位点半醌自由基氢键的突变体的表征。
J Biol Chem. 2007 Mar 23;282(12):8777-85. doi: 10.1074/jbc.M611595200. Epub 2007 Jan 30.
8
Characterization of the exchangeable protons in the immediate vicinity of the semiquinone radical at the QH site of the cytochrome bo3 from Escherichia coli.对来自大肠杆菌的细胞色素bo3的QH位点处半醌自由基紧邻区域可交换质子的表征。
J Biol Chem. 2006 Jun 23;281(25):16879-16887. doi: 10.1074/jbc.M602544200. Epub 2006 Apr 18.
9
The quinone-binding sites of the cytochrome bo3 ubiquinol oxidase from Escherichia coli.来自大肠杆菌的细胞色素bo3泛醇氧化酶的醌结合位点。
Biochim Biophys Acta. 2010 Dec;1797(12):1924-32. doi: 10.1016/j.bbabio.2010.04.011. Epub 2010 Apr 20.
10
Identification of the residues involved in stabilization of the semiquinone radical in the high-affinity ubiquinone binding site in cytochrome bo(3) from Escherichia coli by site-directed mutagenesis and EPR spectroscopy.通过定点诱变和电子顺磁共振光谱法鉴定大肠杆菌细胞色素bo(3)高亲和力泛醌结合位点中参与稳定半醌自由基的残基。
Biochemistry. 2002 Aug 27;41(34):10675-9. doi: 10.1021/bi012146w.
引用本文的文献
1
Cryo-EM structures of cytochrome reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site.细胞色素 c 的冷冻电镜结构显示在一个动态的底物结合位点中存在结合的磷脂和泛醌-8。
Proc Natl Acad Sci U S A. 2021 Aug 24;118(34). doi: 10.1073/pnas.2106750118.
2
Structure of the cytochrome -600 heme-copper menaquinol oxidase bound to inhibitor HQNO shows TM0 is part of the quinol binding site.与抑制剂 HQNO 结合的细胞色素 -600 血红素铜泛醌氧化酶的结构表明 TM0 是醌结合位点的一部分。
Proc Natl Acad Sci U S A. 2020 Jan 14;117(2):872-876. doi: 10.1073/pnas.1915013117. Epub 2019 Dec 30.
3
Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo from Escherichia coli.Q波段电子-核双共振揭示平面外氢键稳定大肠杆菌细胞色素bo中的阴离子泛半醌。
Biochemistry. 2016 Oct 11;55(40):5714-5725. doi: 10.1021/acs.biochem.6b00669. Epub 2016 Sep 28.
4
Defining a direction: electron transfer and catalysis in Escherichia coli complex II enzymes.确定一个方向：大肠杆菌复合物II酶中的电子转移与催化作用
Biochim Biophys Acta. 2013 May;1827(5):668-78. doi: 10.1016/j.bbabio.2013.01.010. Epub 2013 Feb 8.
5
Interactions of intermediate semiquinone with surrounding protein residues at the Q(H) site of wild-type and D75H mutant cytochrome bo3 from Escherichia coli.野生型和 D75H 突变型大肠杆菌细胞色素 bo3 的 Q(H) 部位中间半醌与周围蛋白残基的相互作用。
Biochemistry. 2012 May 8;51(18):3827-38. doi: 10.1021/bi300151q. Epub 2012 Apr 22.
6
A rapid and robust method for selective isotope labeling of proteins.一种快速而稳健的蛋白质选择性同位素标记方法。
Methods. 2011 Dec;55(4):370-8. doi: 10.1016/j.ymeth.2011.08.019. Epub 2011 Sep 8.
7
Exploring by pulsed EPR the electronic structure of ubisemiquinone bound at the QH site of cytochrome bo3 from Escherichia coli with in vivo 13C-labeled methyl and methoxy substituents.通过脉冲 EPR 探索在体内用 13C 标记的甲基和甲氧基取代基结合在大肠杆菌细胞色素 bo3 的 QH 位点的半醌的电子结构。
J Biol Chem. 2011 Mar 25;286(12):10105-14. doi: 10.1074/jbc.M110.206821. Epub 2011 Jan 19.
8
Hydrogen bonds between nitrogen donors and the semiquinone in the Q(B) site of bacterial reaction centers.供体氮原子与细菌反应中心 Q(B)部位半醌之间的氢键。
J Am Chem Soc. 2010 Aug 25;132(33):11671-7. doi: 10.1021/ja104134e.
9
The quinone-binding sites of the cytochrome bo3 ubiquinol oxidase from Escherichia coli.来自大肠杆菌的细胞色素bo3泛醇氧化酶的醌结合位点。
Biochim Biophys Acta. 2010 Dec;1797(12):1924-32. doi: 10.1016/j.bbabio.2010.04.011. Epub 2010 Apr 20.
10
Characterization of the semiquinone radical stabilized by the cytochrome aa3-600 menaquinol oxidase of Bacillus subtilis.枯草芽孢杆菌细胞色素aa3-600甲萘醌氧化酶稳定的半醌自由基的表征
J Biol Chem. 2010 Jun 11;285(24):18241-51. doi: 10.1074/jbc.M110.116186. Epub 2010 Mar 29.
本文引用的文献
1
Characterization of mutants that change the hydrogen bonding of the semiquinone radical at the QH site of the cytochrome bo3 from Escherichia coli.对改变大肠杆菌细胞色素bo3的QH位点半醌自由基氢键的突变体的表征。
J Biol Chem. 2007 Mar 23;282(12):8777-85. doi: 10.1074/jbc.M611595200. Epub 2007 Jan 30.
2
Protein-cofactor interactions and EPR parameters for the Q(H) quinone binding site of quinol oxidase. A density functional study.喹醇氧化酶Q(H)醌结合位点的蛋白质-辅因子相互作用及电子顺磁共振参数。一项密度泛函研究。
J Am Chem Soc. 2006 May 3;128(17):5659-71. doi: 10.1021/ja053988b.
3
Characterization of the exchangeable protons in the immediate vicinity of the semiquinone radical at the QH site of the cytochrome bo3 from Escherichia coli.对来自大肠杆菌的细胞色素bo3的QH位点处半醌自由基紧邻区域可交换质子的表征。
J Biol Chem. 2006 Jun 23;281(25):16879-16887. doi: 10.1074/jbc.M602544200. Epub 2006 Apr 18.
4
Asymmetric binding of the high-affinity Q(H)(*)(-) ubisemiquinone in quinol oxidase (bo3) from Escherichia coli studied by multifrequency electron paramagnetic resonance spectroscopy.利用多频电子顺磁共振光谱研究大肠杆菌喹醇氧化酶（bo3）中高亲和力Q(H)(*)(-) 泛半醌的不对称结合。
Biochemistry. 2003 May 20;42(19):5632-9. doi: 10.1021/bi034010z.
5
Identification of the residues involved in stabilization of the semiquinone radical in the high-affinity ubiquinone binding site in cytochrome bo(3) from Escherichia coli by site-directed mutagenesis and EPR spectroscopy.通过定点诱变和电子顺磁共振光谱法鉴定大肠杆菌细胞色素bo(3)高亲和力泛醌结合位点中参与稳定半醌自由基的残基。
Biochemistry. 2002 Aug 27;41(34):10675-9. doi: 10.1021/bi012146w.
6
Direct evidence for the protonation of aspartate-75, proposed to be at a quinol binding site, upon reduction of cytochrome bo3 from Escherichia coli.在还原来自大肠杆菌的细胞色素bo3时，天冬氨酸-75质子化的直接证据，该天冬氨酸-75被认为位于醌结合位点。
Biochemistry. 2001 Jan 30;40(4):1077-82. doi: 10.1021/bi002154x.
7
QH*- ubisemiquinone radical in the bo3-type ubiquinol oxidase studied by pulsed electron paramagnetic resonance and hyperfine sublevel correlation spectroscopy.通过脉冲电子顺磁共振和超精细能级相关光谱研究的bo3型泛醇氧化酶中的QH* - 半醌自由基。
Biochemistry. 2001 Jan 30;40(4):1037-43. doi: 10.1021/bi001641+.
8
Probing molecular structure of dioxygen reduction site of bacterial quinol oxidases through ligand binding to the redox metal centers.
J Inorg Biochem. 2000 Nov;82(1-4):19-25. doi: 10.1016/s0162-0134(00)00140-9.
9
The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site.来自大肠杆菌的泛醇氧化酶的结构及其泛醌结合位点。
Nat Struct Biol. 2000 Oct;7(10):910-7. doi: 10.1038/82824.
10
Vibrational modes of ubiquinone in cytochrome bo(3) from Escherichia coli identified by Fourier transform infrared difference spectroscopy and specific (13)C labeling.通过傅里叶变换红外差光谱和特定的¹³C标记鉴定大肠杆菌细胞色素bo(3)中泛醌的振动模式。
Biochemistry. 1999 Nov 2;38(44):14683-9. doi: 10.1021/bi991267h.
Zotero 插件