Molecular mechanism of ADP-ribose hydrolysis by human NUDT5 from structural and kinetic studies
文献类型：期刊论文
| 作者 | Zha, MW; Guo, Q; Zhang, YC; Yu, B; Ou, Y; Zhong, C; Ding, JP |
| 刊名 | JOURNAL OF MOLECULAR BIOLOGY
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| 出版日期 | 2008 |
| 卷号 | 379期号:3页码:568-578 |
| 关键词 | nudix domain ADPR ADP-ribose pyrophosphatase NUDT5 molecular mechanism |
| 通讯作者 | Zhong, C (reprint author), Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Biochem & Cell Biol, State Key Lab Mol Biol, 320 Yue Yang Rd, Shanghai 200031, Peoples R China.,czhong@sibs.ac.cn ; jpding@sibs.ac.cn |
| 英文摘要 | Human NUDT5 (hNUDT5) is an ADP-ribose (ADPR) pyrophosphatase (ADPRase) that plays important roles in controlling the intracellular levels of ADPR and preventing non-enzymatic ADP-ribosylation of proteins by hydrolyzing ADPR to AMP and ribose 5'-phosphate. We report the crystal structure of hNUDT5 in complex with a non-hydrolyzable ADPR analogue, alpha,beta-methyleneadenosine diphosphoribose, and three Mg2+ ions representing the transition state of the enzyme during catalysis. Analysis of this structure and comparison with previously reported hNUDT5 structures identify key residues involved in substrate binding and catalysis. In the transition-state structure, three metal ions are bound at the active site and are coordinated by surrounding residues and water molecules. A conserved water molecule is at an ideal position for nucleophilic attack on the a-phosphate of ADPR. The side chain of Glu166 on loop L9 changes its conformation to interact with the conserved water molecule compared with that in the substrate-bound structure and appears to function as a catalytic base. Mutagenesis and kinetic studies show that Trp28 and Trp46 are important for the substrate binding; Arg51 is involved in both the substrate binding and the catalysis; and Glu112 and Glu116 of the Nudix motif, Glu166 on loop L9, and Arg111 are critical for the catalysis. The structural and biochemical data together reveal the molecular basis of the catalytic mechanism of ADPR hydrolysis by hNUDT5. Specifically, Glu166 functions as a catalytic base to deprotonate a conserved water molecule that acts as a nucleophile to attack the alpha-phosphate of ADPR, and three Mg2+ ions are involved in the activation of the nucleophile and the binding of the substrate. Structural comparison of different ADPRases also suggests that most dimeric ADPRases may share a similar catalytic mechanism of ADPR hydrolysis. (c) 2008 Elsevier Ltd. All rights reserved. |
| 学科主题 | Biochemistry & Molecular Biology |
| 类目[WOS] | Biochemistry & Molecular Biology |
| 关键词[WOS] | NUDIX HYDROLASES ; CRYSTAL-STRUCTURES ; PYROPHOSPHATASE ; RIBOSYLATION ; SUBSTRATE ; CLONING ; EXPRESSION ; INSIGHTS ; FAMILY |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000256586500015 |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.143/handle/331003/1354]  |
| 专题 | 上海生化细胞研究所_上海生科院生化细胞研究所 |
| 推荐引用方式 GB/T 7714 | Zha, MW,Guo, Q,Zhang, YC,et al. Molecular mechanism of ADP-ribose hydrolysis by human NUDT5 from structural and kinetic studies[J]. JOURNAL OF MOLECULAR BIOLOGY,2008,379(3):568-578. |
| APA | Zha, MW.,Guo, Q.,Zhang, YC.,Yu, B.,Ou, Y.,...&Ding, JP.(2008).Molecular mechanism of ADP-ribose hydrolysis by human NUDT5 from structural and kinetic studies.JOURNAL OF MOLECULAR BIOLOGY,379(3),568-578. |
| MLA | Zha, MW,et al."Molecular mechanism of ADP-ribose hydrolysis by human NUDT5 from structural and kinetic studies".JOURNAL OF MOLECULAR BIOLOGY 379.3(2008):568-578. |
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