Crystal structure of the archaeosine synthase QueF-like-Insights into amidino transfer and tRNA recognition by the tunnel fold.
Crystal structure of the archaeosine synthase QueF-like-Insights into amidino transfer and tRNA recognition by the tunnel fold.
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DOI：
10.1002/prot.25202
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发表时间：
2017-01
影响因子：
2.9
通讯作者：
Swairjo, Manal A.
中科院分区：
文献类型：
--
作者：
Mei, Xianghan;Alvarez, Jonathan;Bon Ramos, Adriana;Samanta, Uttamkumar;Iwata-Reuyl, Dirk;Swairjo, Manal A.
关键词：
隧道折叠(T-折叠)结构超家族是一种具有不同催化活性的多功能蛋白质支架。这在7-去氮鸟苷修饰的核苷tRNA、Queuosine和Archosine的途径中尤其明显。在这些途径中已经确认了T-折叠超家族的四个成员，在这里我们报告了第五个酶的晶体结构：最近发现的氨基转移酶QUF-样(QUF-L)，负责在Crenarocota的一个子集的tRNA的D-环中生物合成考古素的最后一步。QUF-L催化前Q0修饰的tRNA的7-氰基-7-去氮鸟嘌呤(PreQ0)碱基的氰基转化为甲酰胺基。在preQ0存在的情况下确定的结构揭示了两个面对面的五聚体亚基的对称T-折叠同种异构体，在单体间界面有10个活性部位。结合的preQ0与一个保守的活性部位半胱氨酸形成稳定的共价硫酰亚胺键，类似于先前在氰基还原酶QueF中观察到的中间体。尽管这两种酶具有不同的催化功能、系统发育分布和只有19%的序列同源性，但它们共享一个共同的前Q0结合口袋，并且可能是硫代亚胺形成的共同机制。然而，由于其十聚体的紧密扭曲，QUF-L缺乏QUF中存在的NADPH结合位点。大的正电荷分子表面和对接模型表明多个tRNA分子同时结合，并通过表面凹槽对D-环进行结构特异性识别。该结构揭示了丁腈酰胺化的机理，以及共同折叠中不同化学成分的演变。
The tunneling-fold (T-fold) structural superfamily has emerged as a versatile protein scaffold of diverse catalytic activities. This is especially evident in the pathways to the 7-deazaguanosine modified nucleosides of tRNA queuosine and archaeosine. Four members of the T-fold superfamily have been confirmed in these pathways and here we report the crystal structure of a fifth enzyme; the recently discovered amidinotransferase QueF-Like (QueF-L), responsible for the final step in the biosynthesis of archaeosine in the D-loop of tRNA in a subset of Crenarchaeota. QueF-L catalyzes the conversion of the nitrile group of the 7-cyano-7-deazaguanine (preQ0) base of preQ0-modified tRNA to a formamidino group. The structure, determined in the presence of preQ0, reveals a symmetric T-fold homodecamer of two head-to-head facing pentameric subunits, with 10 active sites at the inter-monomer interfaces. Bound preQ0 forms a stable covalent thioimide bond with a conserved active site cysteine similar to the intermediate previously observed in the nitrile reductase QueF. Despite distinct catalytic functions, phylogenetic distributions, and only 19% sequence identity, the two enzymes share a common preQ0 binding pocket, and likely a common mechanism of thioimide formation. However, due to tight twisting of its decamer, QueF-L lacks the NADPH binding site present in QueF. A large positively charged molecular surface and a docking model suggest simultaneous binding of multiple tRNA molecules and structure-specific recognition of the D-loop by a surface groove. The structure sheds light on the mechanism of nitrile amidation, and the evolution of diverse chemistries in a common fold.
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影响因子：
4.8
作者：
Chikwana, Vimbai M.;Stec, Boguslaw;Swairjo, Manal A.
通讯作者：
Swairjo, Manal A.
影响因子：
64.5
作者：
Ishitani, R;Nureki, O;Yokoyama, S
通讯作者：
Yokoyama, S
影响因子：
2.9
作者：
McCarty, Reid M.;Somogyi, Arpad;Lin, Guangxin;Jacobsen, Neil E.;Bandarian, Vahe
通讯作者：
Bandarian, Vahe
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
影响因子：
2.9
作者：
McCarty, Reid M.;Somogyi, Arpad;Bandarian, Vahe
通讯作者：
Bandarian, Vahe