Ring Contraction Catalyzed by the Metal-Dependent Radical SAM Enzyme: 7-Carboxy-7-deazaguanine Synthase from B. multivorans. Theoretical Insights into the Reaction Mechanism and the Influence of Metal Ions
文献类型：期刊论文
| 作者 | Zhu, Wenyou1; Liu, Yongjun1,2 |
| 刊名 | acs catalysis
 |
| 出版日期 | 2015-07-01 |
| 卷号 | 5期号:7页码:3953-3965 |
| 关键词 | 7-carboxy-7-deazaguanine synthase (QueE) reaction mechanism 7-carboxy-7-deazaguanine (CDG) 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) QM/MM SAM radical enzyme |
| 中文摘要 | 7-carboxy-7-deazaguanine synthase (quee) is a radical s-adenosylmethionine (sam) enzyme that catalyzes the conversion of 6-carboxy-5,6,7,8-tetrahydropterin (cph4) to 7-carboxy-7-deazaguanine (cdg). quee also shows a clear dependence on mg2+ ion and is considered a new feature for a radical sam enzyme. the catalytic mechanism of quee from b. multivorans has been studied using a combined quantum mechanics and molecular mechanics (qm/mm) method. the results of our calculations reveal that the key ring-contraction step involves a bridged intermediate rather than a ring-opening one. for the quee-mg2+ system, the elimination of ammonia is calculated to be rate limiting with a free energy barrier of 18.8 kcal/mol, which is basically in accordance with the estimated value (20.9 kcal/mol) from the experiment. for quee-na+ complex, the rate-limiting step switches to the formation of the bridged intermediate with an energy barrier of 29.3 kcal/mol. natural population analysis indicates that the metal ions do not act as lewis acids; therefore, they mainly play a role in fixing the substrate in its reactive conformation. the different coordination of mg2+ and na+ with the substrate is suggested to be the main reason for leading to the different activities of quee-mg2+ and quee-na+ complexes. |
| 英文摘要 | 7-carboxy-7-deazaguanine synthase (quee) is a radical s-adenosylmethionine (sam) enzyme that catalyzes the conversion of 6-carboxy-5,6,7,8-tetrahydropterin (cph4) to 7-carboxy-7-deazaguanine (cdg). quee also shows a clear dependence on mg2+ ion and is considered a new feature for a radical sam enzyme. the catalytic mechanism of quee from b. multivorans has been studied using a combined quantum mechanics and molecular mechanics (qm/mm) method. the results of our calculations reveal that the key ring-contraction step involves a bridged intermediate rather than a ring-opening one. for the quee-mg2+ system, the elimination of ammonia is calculated to be rate limiting with a free energy barrier of 18.8 kcal/mol, which is basically in accordance with the estimated value (20.9 kcal/mol) from the experiment. for quee-na+ complex, the rate-limiting step switches to the formation of the bridged intermediate with an energy barrier of 29.3 kcal/mol. natural population analysis indicates that the metal ions do not act as lewis acids; therefore, they mainly play a role in fixing the substrate in its reactive conformation. the different coordination of mg2+ and na+ with the substrate is suggested to be the main reason for leading to the different activities of quee-mg2+ and quee-na+ complexes. |
| WOS标题词 | science & technology ; physical sciences |
| 类目[WOS] | chemistry, physical |
| 研究领域[WOS] | chemistry |
| 关键词[WOS] | s-adenosylmethionine enzymes ; transfer-ribonucleic-acid ; lyase activating enzyme ; unique iron site ; pk(a) values ; transfer-rna ; protein superfamily ; nucleoside-q ; biosynthesis ; qm/mm |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000357626800007 |
| 源URL | [http://ir.nwipb.ac.cn/handle/363003/5539]  |
| 专题 | 西北高原生物研究所_中国科学院西北高原生物研究所 |
| 作者单位 | 1.Shandong Univ, Sch Chem & Chem Engn, Key Lab Colloid & Interface Chem, Minist Educ, Jinan 250100, Shandong, Peoples R China 2.Chinese Acad Sci, Northwest Inst Plateau Biol, Key Lab Tibetan Med Res, Xining 810001, Qinghai, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zhu, Wenyou,Liu, Yongjun. Ring Contraction Catalyzed by the Metal-Dependent Radical SAM Enzyme: 7-Carboxy-7-deazaguanine Synthase from B. multivorans. Theoretical Insights into the Reaction Mechanism and the Influence of Metal Ions[J]. acs catalysis,2015,5(7):3953-3965. |
| APA | Zhu, Wenyou,&Liu, Yongjun.(2015).Ring Contraction Catalyzed by the Metal-Dependent Radical SAM Enzyme: 7-Carboxy-7-deazaguanine Synthase from B. multivorans. Theoretical Insights into the Reaction Mechanism and the Influence of Metal Ions.acs catalysis,5(7),3953-3965. |
| MLA | Zhu, Wenyou,et al."Ring Contraction Catalyzed by the Metal-Dependent Radical SAM Enzyme: 7-Carboxy-7-deazaguanine Synthase from B. multivorans. Theoretical Insights into the Reaction Mechanism and the Influence of Metal Ions".acs catalysis 5.7(2015):3953-3965. |
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来源：西北高原生物研究所
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