Modeling of Phosphoribosylpyrophosphate Synthetase from Thermus Thermophilus in Complex with ATP and Ribose 5-Phosphate

Podshivalov D. D.; Sidorov-Biryukov D. D.; Timofeev V. I.; Litunov A. A.; Kostromina M. A.; Sinitsyna K. V.; Muravieva T. I.; Kuranova I. P.; Esipov R. S.

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Modeling of Phosphoribosylpyrophosphate Synthetase from Thermus Thermophilus in Complex with ATP and Ribose 5-Phosphate

机译：用ATP和核糖5-磷酸盐在复合物中磷杂化磷酸盐合成酶的建模

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The positions of the substrates (ATP and ribose 5 phosphate) of phosphoribosylpyrophosphate synthetase from Thermus thermophilus were determined by molecular dynamics simulations. The simulation brought the system to an equilibrium state, with the binding poses of the ligands in the active site being stable. Based on the results of simulation of the complex, the environment of the substrates was analyzed and the amino-acid residues of the enzyme that form polar interactions with the substrates were identified. Candidate sites for mutagenesis, which can be mutated in order to broaden the substrate specificity toward ribose 5-phosphate, are proposed.

机译：通过分子动力学模拟测定来自热嗜热磷酸磷酸磷酸亚磷酸酯合成酶的亚磷酸亚磷苷磷酸盐合成酶的位置。该模拟将该系统带到平衡状态，在活性位点中的配体的结合姿势是稳定的。基于复合物的模拟结果，分析了基材的环境，并鉴定了与基材形成极性相互作用的酶的氨基酸残基。提出了诱变的候选位点，其可以突变以促进朝向核糖5-磷酸核苷酸的底物特异性。

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《Crystallography reports》 |2019年第1期|共4页
作者
Podshivalov D. D.; Sidorov-Biryukov D. D.; Timofeev V. I.; Litunov A. A.; Kostromina M. A.; Sinitsyna K. V.; Muravieva T. I.; Kuranova I. P.; Esipov R. S.;
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Russian Acad Moscow Shemyakin Ovchinnikov Inst Bioorgan Chem Moscow 117997 Russia;

Russian Acad Moscow Shemyakin Ovchinnikov Inst Bioorgan Chem Moscow 117997 Russia;

Russian Acad Moscow Shemyakin Ovchinnikov Inst Bioorgan Chem Moscow 117997 Russia;

Russian Acad Moscow Shemyakin Ovchinnikov Inst Bioorgan Chem Moscow 117997 Russia;

Russian Acad Moscow Shemyakin Ovchinnikov Inst Bioorgan Chem Moscow 117997 Russia;

Russian Acad Moscow Shemyakin Ovchinnikov Inst Bioorgan Chem Moscow 117997 Russia;

Russian Acad Moscow Shemyakin Ovchinnikov Inst Bioorgan Chem Moscow 117997 Russia;

Russian Acad Moscow Shemyakin Ovchinnikov Inst Bioorgan Chem Moscow 117997 Russia;

Russian Acad Moscow Shemyakin Ovchinnikov Inst Bioorgan Chem Moscow 117997 Russia;

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1. Modeling of Phosphoribosylpyrophosphate Synthetase from Thermus Thermophilus in Complex with ATP and Ribose 5-Phosphate [J] . Podshivalov D. D., Sidorov-Biryukov D. D., Timofeev V. I., Crystallography reports . 2019,第1期

机译：用ATP和核糖5-磷酸盐在复合物中磷杂化磷酸盐合成酶的建模
2. Phosphoribosylpyrophosphate synthetase (PrsA) variants alter cellular pools of ribose 5-phosphate and influence thiamine synthesis in Salmonella enterica [J] . Mark J. Koenigsknecht, Luke A. Fenlon, Diana M. Downs Microbiology . 2010,第5期

机译：磷酰杂磷酸盐合成酶（PRSA）变体改变核糖5-磷酸盐的细胞库，并影响沙门氏菌肠道的硫胺素合成
3. Crystallization and Preliminary X-ray Diffraction Analysis of Recombinant Phosphoribosylpyrophosphate Synthetase from the Thermophilic Thermus Thermophilus Strain HB27 [J] . Abramchik Yu. A., Timofeev V. I., Muravieva T. I., Crystallography reports . 2017,第1期

机译：嗜热热药物菌株HB27结晶及重组磷杂丝亚磷酸盐合成酶的结晶及初步X射线衍射分析
4. The Crystal Structure Of Thermus Thermophilus Tyrosyl-tRNA Syntheyase Complexed With tRNAtyr [C] . 19th tRNA workshop tRNA 2002"" . 2002

机译：嗜热栖热菌酪氨酰-tRNA合成酶与tRNAtyr复合的晶体结构
5. Functional characterization of Leishmania infantum asparagine synthetase A and ribose 5-phosphate isomerase B as potential drug targets [D] . Faria, Joana Raquel Correia. 2016

机译：婴儿利什曼原虫天冬酰胺合成酶A和核糖5-磷酸异构酶B作为潜在药物靶标的功能表征
6. Crystal structure of recombinant phosphoribosylpyrophosphate synthetase 2 from Thermus thermophilus HB27 complexed with ADP and sulfate ions [O] . Vladimir I. Timofeev, Ekaterina V. Sinitsyna, Maria A. Kostromina, 2017

机译：嗜热栖热菌HB27重组磷酸核糖焦磷酸合成酶2与ADP和硫酸根离子复合的晶体结构
7. Phosphoribosylpyrophosphate synthetase (PrsA) variants alter cellular pools of ribose 5-phosphate and influence thiamine synthesis in Salmonella enterica [O] . Koenigsknecht, Mark J., Fenlon, Luke A., Downs, Diana M. 2010

机译：磷酸核糖焦磷酸合成酶（PrsA）变异 5-磷酸核糖的细胞池并影响硫胺素的合成在肠沙门氏菌

Modeling of Phosphoribosylpyrophosphate Synthetase from Thermus Thermophilus in Complex with ATP and Ribose 5-Phosphate

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