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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 | |
Zhu, Wenyou1; Liu, Yongjun1,2 | |
2015-07-01 | |
发表期刊 | ACS CATALYSIS |
卷号 | 5期号:7页码:3953-3965 |
文章类型 | Article |
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.; 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. |
关键词 | 7-carboxy-7-deazaguanine Synthase (Quee) Reaction Mechanism 7-carboxy-7-deazaguanine (Cdg) Qm/mm 6-carboxy-5 Sam Radical Enzyme 6 7 8-tetrahydropterin (Cph4) |
WOS标题词 | Science & Technology ; Physical Sciences |
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研究方向 | Chemistry |
WOS类目 | Chemistry, Physical |
WOS记录号 | WOS:000357626800007 |
引用统计 | |
文献类型 | 期刊论文 |
条目标识符 | http://210.75.249.4/handle/363003/5539 |
专题 | 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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