Structural and functional investigation of flavin binding center of the NqrC subunit of sodium-translocating NADH:quinone oxidoreductase from Vibrio harveyi.
Structural and functional investigation of flavin binding center of the NqrC subunit of sodium-translocating NADH:quinone oxidoreductase from Vibrio harveyi.
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DOI：
10.1371/journal.pone.0118548
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Gordeliy V
中科院分区：
文献类型：
--
作者：
Borshchevskiy V;Round E;Bertsova Y;Polovinkin V;Gushchin I;Ishchenko A;Kovalev K;Mishin A;Kachalova G;Popov A;Bogachev A;Gordeliy V
Na+-转位NADH：苯醌氧化还原酶(NQR)是一种氧化还原驱动的钠泵，在包括病原菌在内的各种细菌的呼吸链中工作。该酶有一组独特的氧化还原活性辅基，包括两个共价结合的黄素单核苷酸(FMN)残基，连接在NqrB和NqrC亚基的苏氨酸残基上。亚基中FMN共价键的形成原因尚未确定。在目前的工作中，研究了自由FMN与来自哈维氏弧菌的NqrC脱辅基形式的结合，发现在没有共价键的情况下，NqrC与FMN的亲和力很低。为了研究NqrC中黄素结合的结构，对其全息形式进行了晶化，并在1.56？分辨率下对其三维结构进行了求解。研究发现，FMN残基的异四氧嘧啶部分被埋入疏水空腔中，其嘧啶环被挤压在疏水氨基酸残基之间，而其苯环从蛋白质环境中延伸出来。黄素结合口袋的这种结构似乎提供了苯环的灵活性，这可以帮助FMN残基形成弯曲的构象，从而稳定假体基团的单电子还原形式。这些性质也可能导致黄素的非共价结合相对较弱。这一事实以及绝大多数NqrC样蛋白中FMN结合域的周质位置可能解释了为什么有必要通过共价键来防止这个修复基团丢失到外部介质中。
Na+-translocating NADH:quinone oxidoreductase (NQR) is a redox-driven sodium pump operating in the respiratory chain of various bacteria, including pathogenic species. The enzyme has a unique set of redox active prosthetic groups, which includes two covalently bound flavin mononucleotide (FMN) residues attached to threonine residues in subunits NqrB and NqrC. The reason of FMN covalent bonding in the subunits has not been established yet. In the current work, binding of free FMN to the apo-form of NqrC from Vibrio harveyi was studied showing very low affinity of NqrC to FMN in the absence of its covalent bonding. To study structural aspects of flavin binding in NqrC, its holo-form was crystallized and its 3D structure was solved at 1.56 Å resolution. It was found that the isoalloxazine moiety of the FMN residue is buried in a hydrophobic cavity and that its pyrimidine ring is squeezed between hydrophobic amino acid residues while its benzene ring is extended from the protein surroundings. This structure of the flavin-binding pocket appears to provide flexibility of the benzene ring, which can help the FMN residue to take the bended conformation and thus to stabilize the one-electron reduced form of the prosthetic group. These properties may also lead to relatively weak noncovalent binding of the flavin. This fact along with periplasmic location of the FMN-binding domains in the vast majority of NqrC-like proteins may explain the necessity of the covalent bonding of this prosthetic group to prevent its loss to the external medium.
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影响因子：
3.5
作者：
HAYASHI, M;HIRAI, K;UNEMOTO, T
通讯作者：
UNEMOTO, T
影响因子：
2.9
作者：
Li, Xi;Chow, Dar-Chone;Tu, Shiao-Chun
通讯作者：
Tu, Shiao-Chun
影响因子：
4.3
作者：
Verkhovsky, Michael I.;Bogachev, Alexander V.
通讯作者：
Bogachev, Alexander V.
DOI：
10.1107/s2053230x14009881
发表时间：
2014-07-01
影响因子：
0.9
作者：
Vohl, Georg;Nedielkov, Ruslan;Fritz, Guenter
通讯作者：
Fritz, Guenter
DOI：
10.1107/s0907444909052925
发表时间：
2010-02
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Adams PD;Afonine PV;Bunkóczi G;Chen VB;Davis IW;Echols N;Headd JJ;Hung LW;Kapral GJ;Grosse-Kunstleve RW;McCoy AJ;Moriarty NW;Oeffner R;Read RJ;Richardson DC;Richardson JS;Terwilliger TC;Zwart PH
通讯作者：
Zwart PH