Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms2io6A37 in tRNA
Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms2io6A37 in tRNA
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DOI：
10.1002/prot.21640
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发表时间：
2008-01-01
影响因子：
2.9
通讯作者：
Bujnicki, Janusz M.
中科院分区：
文献类型：
--
作者：
Kaminska, Katarzyna H.;Baraniak, Urszula;Bujnicki, Janusz M.
所有生物体的tRNA都含有转录后修饰的核苷，这些核苷来源于四种典型的核苷。在大多数读取以Q开始的密码子的tRNA中，与反密码子的3'位置相邻的位置37处的腺苷被修饰为N-6-（Δ（2）-异戊烯基）腺苷（i（6）A）。在许多细菌中，如大肠杆菌，该残基通常高度修饰为N-6-异戊烯基-2-硫代甲基腺苷（ms（2）i（6）A）。在一些细菌中，如鼠伤寒沙门氏菌，ms（2）i（6）A可进一步羟基化为N-6（cis-4-hydroxyisopentenyl）-2-thiomethyladenosine（ms（2）io（6）A）。虽然已经鉴定了引入相应修饰的酶（异戊烯基转移酶MiaA、甲硫基转移酶MiaB和羟化酶MiaE），但是它们的结构仍然未知，并且序列-功能关系仍然模糊。我们使用蛋白质折叠识别方法对MiaA、MiaB和MiaE进行了序列分析和结构预测。然后使用新的建模协议建立所有三种蛋白质的三维模型，该协议旨在克服模板之间的比对和分歧的不确定性。对于MiaA和MiaB，分别基于来自P-环NTR和Radical-SAM超家族的模板构建催化核心。对于MiaB，我们还模拟了C-末端TRAM结构域和新预测的N-末端黄素氧还蛋白折叠结构域。对于MiaE，我们自信地预测，它与铁蛋白样四螺旋束蛋白共享三维折叠，并且它与二铁羧酸酶，特别是催化烷烃生物羟基化的甲烷单加氧酶（E.C.1.14.13.25）具有相似的活性位点和作用机制。我们的模型为参与i（6）A、ms（2）i（6）A和ms（2）io（6）A生物合成的酶提供了第一个结构平台，解释了文献中的数据，并将有助于设计进一步的实验和解释其结果。
tRNAs from all organisms contain posttranscriptionally modified nucleosides, which are derived from the four canonical nucleosides. In most tRNAs that read codons beginning with Q, adenosine in the position 37 adjacent to the 3' position of the anticodon is modified to N-6-(Delta(2)-isopentenyl) adenosine (i(6)A). In many bacteria, such as Escherichia coli, this residue is typically hypermodifted to N-6-isopentenyl-2-thiomethyladenosine (ms(2)i(6)A). In a few bacteria, such as Salmonella typhimurium, ms(2)i(6)A can be further hydroxy- lated to N-6(cis-4-hydroxyisopen tenyl)-2-thiomethyladenosine (ms(2)io(6)A). Although the enzymes that introduce the respective modifications (prenyltransferase MiaA, methylthio transferase MiaB, and hydroxylase MiaE) have been identified, their structures remain unknown and sequence-function relationships remain obscure. We carried out sequence analysis and structure prediction of MiaA, MiaB, and MiaE, using the protein fold-recognition approach. Three-dimensional models of all three proteins were then built using a new modeling protocol designed to overcome uncertainties in the alignments and divergence between the templates. For MiaA and MiaB, the catalytic core was built based on the templates from the P-loop NTPase and Radical-SAM superfamilies, respectively. For MiaB, we have also modeled the C-terminal TRAM domain and the newly predicted N-terminal flavodoxin-fold domain. For MiaE, we confidently predict that it shares the three-dimensional fold with the ferritin-like four-helix bundle proteins and that it has a similar active site and mechanism of action to diiron carboxylate enzymes, in particular, methane monooxygenase (E.C.1.14.13.25) that catalyses the biological hydroxylation of alkanes. Our models provide the first structural platform for enzymes involved in the biosynthesis of i(6)A, ms(2)i(6)A, and ms(2)io(6)A, explain the data available from the literature and will help to design further experiments and interpret their results.