Citation: Zhang Yu, Yang Xinya, Yu Haiying, Ma Guangcai. Theoretical Insight into the Catalytic Mechanism of Enoyl-CoA Hydratase[J]. Acta Chimica Sinica, ;2017, 75(5): 494-500. doi: 10.6023/A16100559 shu

Theoretical Insight into the Catalytic Mechanism of Enoyl-CoA Hydratase

College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China

Corresponding author: Ma Guangcai, magc@zjnu.edu.cn
Received Date: 20 October 2016

Fund Project: the Natural Science Foundation of Zhejiang Province LY16B070002Technological Innovation Plan & New Talent Plan for College Students in Zhejiang Province 2015R404006

Figures(7)

Enoyl-CoA hydratase (ECH), which is also known as crotonase, is the second requisite enzyme in the β-oxidation pathway of fatty acid that catalyzes the syn hydration of α, β-unsaturated thiolester substrates. In this work, ECH-catalyzed hydration mechanisms of DAC-CoA and Crotonyl-CoA were investigated using density functional theory (DFT) methods. Geometrical structures were optimized using Gaussian 03 program at the B3LYP/6-31G(d, p) level of theory. Frequency calculations were performed with the 6-31G(d, p) basis set to obtain zero-point vibrational energies (ZPEs) and to confirm the nature of all the stationary points that have no imaginary frequency for the local minima and have only one imaginary frequency for the saddle points. The single-point calculations on the optimized geometries were further performed with 6-311++G(2d, 2p) basis set to obtain more accurate energies. The polarizable-continuum model (PCM) with the dielectric constant of 4 was used to calculate the single point energies at 6-311++G(2d, p) level on all the optimized geometries to consider the effects of enzymatic environment that was not included in the computational model. Considering that B3LYP functional lacks the proper description of the long-range dispersion interactions, we further used the DFT-D3 program to calculate the empirical dispersion correction to correct the B3LYP energies. The final energies reported in this work are the single-point energies corrected for ZPEs, solvation and dispersion effects. The calculated results suggested that hydration proceeds through a stepwise mechanism, involving an enolate intermediate. Glu164 functions as the sole base/acid for catalysis. Although Glu144 is not directly involved in hydration, it induces the catalytic water molecule to locate an ideal orientation to attack the double bond of substrate by the hydrogen-bonding interaction. Crotonyl-CoA shows higher hydration activity than DAC-CoA. The backbone NH groups of Ala98 and Gly141 form an oxyanion hole with substrate carbonyl oxygen, which play key roles in binding substrate and stabilizing the generated transition states and intermediates. In addition, the hydrogen-bonding networks surrounding Glu144 and Glu164 are of great importance for active site arrangement.
- Enoyl-CoA hydratase,
- catalytic mechanism,
- density functional theory,
- DAC-CoA,
- Crotonyl-CoA
1. [1]
  Willadsen, P.; Eggerer, H. Eur. J. Biochem. 1975, 54, 247. doi: 10.1111/ejb.1975.54.issue-1
2. [2]
  Wu, W. J.; Feng, Y.; He, X.; Hofstein, H. A.; Raleigh, D. P.; Tonge, P. J. J. Am. Chem. Soc. 2000, 122, 3987. doi: 10.1021/ja992286h
3. [3]
  Bahnson, B. J.; Anderson, V. E. Biochemistry 1989, 28, 4173. doi: 10.1021/bi00436a008
4. [4]
  Müller-Newen, G.; Janssen, U.; Stoffel, W. Eur. J. Biochem. 1995, 228, 68. doi: 10.1111/ejb.1995.228.issue-1
5. [5]
  Boersma, A. J.; Coquière, D.; Geerdink, D.; Rosati, F.; Feringa, B. L.; Roelfes, G. Nat. Chem. 2010, 2, 991. doi: 10.1038/nchem.819
6. [6]
  Silverman, R. B. The Organic Chemistry of Enzyme-catalyzed Reactions, Academic, London, 2002, pp. 428~448.
7. [7]
  Engel, C. K.; Mathieu, M.; Zeelen, J. P.; Hiltunen, J. K.; Wierenga, R. K. EMBO J. 1996, 15, 5135.
8. [8]
  Bahnson, B. J.; Anderson, V. E.; Petsko, G. A. Biochemistry 2002, 41, 2621. doi: 10.1021/bi015844p
9. [9]
  Hisano, T.; Tsuge, T.; Fukui, T.; Iwata, T.; Miki, K.; Doi, Y. J. Biol. Chem. 2003, 278, 617.
10. [10]
  Koski, M. K.; Haapalainen, A. M.; Hiltunen, J. K.; Glumoff, T. J. Biol. Chem. 2004, 279, 24666. doi: 10.1074/jbc.M400293200
11. [11]
  Baugh, L.; Phan, I.; Begley, D. W.; Clifton, M. C.; Armour, B.; Dranow, D. M.; Taylor, B. M.; Muruthi, M. M.; Abendroth, J.; Fairman, J. W.; Fox, D. 3rd; Dieterich, S. H.; Staker, B. L.; Gardberg, A. S.; Choi, R.; Hewitt, S. N.; Napuli, A. J.; Myers, J.; Barrett, L. K.; Zhang, Y.; Ferrell, M.; Mundt, E.; Thompkins, K.; Tran, N.; Lyons-Abbott, S.; Abramov, A.; Sekar, A.; Serbzhinskiy, D, ; Lorimer, D.; Buchko, G. W.; Stacy, R.; Stewart, L. J.; Edwards, T. E.; Van Voorhis, W. C.; Myler, P. J. Tuberculosis 2015, 95, 142.
12. [12]
  Feng, Y.; Hofstein, H. A.; Zwahlen, J.; Tonge, P. J. Biochemistry 2002, 41, 12883. doi: 10.1021/bi020382g
13. [13]
  Hofstein, H. A.; Feng, Y.; Anderson, V. E.; Tonge, P. J. Biochemistry 1999, 38, 9508. doi: 10.1021/bi990506y
14. [14]
  Engel, C. K.; Kiema, T. R.; Hiltunen, J. K.; Wierenga, R. K. J. Mol. Biol. 1998, 275, 847. doi: 10.1006/jmbi.1997.1491
15. [15]
  Bell, A. F.; Wu, J.; Feng, Y.; Tonge, P. J. Biochemistry 2001, 40, 1725. doi: 10.1021/bi001733z
16. [16]
  D'Ordine, R. L.; Pawlak, J.; Bahnson, B. J.; Anderson, V. E.; Biochemistry 2002, 41, 2630. doi: 10.1021/bi015845h
17. [17]
  Bahnson, B. J.; Anderson, V. E. Biochemistry 1991, 30, 5894. doi: 10.1021/bi00238a013
18. [18]
  Pawlak, J.; Bahnson, B.; Anderson, V. Nukleonika 2002, 47, 33.
19. [19]
  Cui, X.; He, R.; Yang, Q.; Shen, W.; Li, M. J. Mol. Model. 2014, 20, 2411. doi: 10.1007/s00894-014-2411-5
20. [20]
  Agnihotri, G.; Liu, H. W. Bioorg. Med. Chem. 2003, 11, 9. doi: 10.1016/S0968-0896(02)00333-4
21. [21]
  Siegbahn, P. E.; Himo, F. J. Biol. Inorg. Chem. 2009, 14, 643. doi: 10.1007/s00775-009-0511-y
22. [22]
  Siegbahn, P. E.; Blomberg, M. R. Chem. Rev. 2010, 110, 7040. doi: 10.1021/cr100070p
23. [23]
  Hopmann, K. H.; Himo, F. In Comprehensive Natural Products Chemistry Ⅱ Chemistry and Biology, Vol. 8, Eds.: Mander, L. N.; Liu, H.-W., Elsevier, Oxford, 2010, pp. 719~747.
24. [24]
  Siegbahn, P. E.; Himo, F. Wiley Interdisciplinary Reviews: Computational Molecular Science, 2011, 1, 323. doi: 10.1002/wcms.13
25. [25]
  Blomberg, M. R.; Borowski, T.; Himo, F.; Liao, R. Z.; Siegbahn, P. E. Chem. Rev. 2014, 114, 3601. doi: 10.1021/cr400388t
26. [26]
  Becke, A. D. J. Chem. Phys. 1993, 98, 5648. doi: 10.1063/1.464913
27. [27]
  Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785. doi: 10.1103/PhysRevB.37.785
28. [28]
  Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03 (Revision D. 01), Gaussian, Inc., Wallingford CT, 2004.
29. [29]
  Barone, V.; Cossi, M.; Tomasi, J. J. Comput. Chem. 1998, 19, 404. doi: 10.1002/(ISSN)1096-987X
30. [30]
  Tomasi, J.; Persico, M. Chem. Rev. 1994, 94, 2027. doi: 10.1021/cr00031a013
31. [31]
  Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. J. Chem. Phys. 2010, 132, 154104. doi: 10.1063/1.3382344
32. [32]
  Grimme, S.; Ehrlich, S.; Goerigk, L. J. Comput. Chem. 2011, 32, 1456. doi: 10.1002/jcc.v32.7
33. [33]
  D'Ordine, R. L.; Tonge, P. J.; Carey, P. R.; Anderson, V. E. Biochemistry 1994, 33, 12635. doi: 10.1021/bi00208a014
1. [1]
  Yingchun ZHANG , Yiwei SHI , Ruijie YANG , Xin WANG , Zhiguo SONG , Min WANG . Dual ligands manganese complexes based on benzene sulfonic acid and 2, 2′-bipyridine: Structure and catalytic properties and mechanism in Mannich reaction. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1501-1510. doi: 10.11862/CJIC.20240078
2. [2]
  Wen YANG , Didi WANG , Ziyi HUANG , Yaping ZHOU , Yanyan FENG . La promoted hydrotalcite derived Ni-based catalysts: In situ preparation and CO₂ methanation performance. Chinese Journal of Inorganic Chemistry, 2024, 40(3): 561-570. doi: 10.11862/CJIC.20230276
3. [3]
  Qiangqiang SUN , Pengcheng ZHAO , Ruoyu WU , Baoyue CAO . Multistage microporous bifunctional catalyst constructed by P-doped nickel-based sulfide ultra-thin nanosheets for energy-efficient hydrogen production from water electrolysis. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1151-1161. doi: 10.11862/CJIC.20230454
4. [4]
  Zhaoyang WANG , Chun YANG , Yaoyao Song , Na HAN , Xiaomeng LIU , Qinglun WANG . Lanthanide(Ⅲ) complexes derived from 4′-(2-pyridyl)-2, 2′∶6′, 2″-terpyridine: Crystal structures, fluorescent and magnetic properties. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1442-1451. doi: 10.11862/CJIC.20240114
5. [5]
  Guangming YIN , Huaiyao WANG , Jianhua ZHENG , Xinyue DONG , Jian LI , Yi'nan SUN , Yiming GAO , Bingbing WANG . Preparation and photocatalytic degradation performance of Ag/protonated g-C₃N₄ nanorod materials. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1491-1500. doi: 10.11862/CJIC.20240086
6. [6]
  Yuhao SUN , Qingzhe DONG , Lei ZHAO , Xiaodan JIANG , Hailing GUO , Xianglong MENG , Yongmei GUO . Synthesis and antibacterial properties of silver-loaded sod-based zeolite. Chinese Journal of Inorganic Chemistry, 2024, 40(4): 761-770. doi: 10.11862/CJIC.20230169
7. [7]
  Doudou Qin , Junyang Ding , Chu Liang , Qian Liu , Ligang Feng , Yang Luo , Guangzhi Hu , Jun Luo , Xijun Liu . Addressing Challenges and Enhancing Performance of Manganese-based Cathode Materials in Aqueous Zinc-Ion Batteries. Acta Physico-Chimica Sinica, 2024, 40(10): 2310034-. doi: 10.3866/PKU.WHXB202310034
8. [8]
  Lu XU , Chengyu ZHANG , Wenjuan JI , Haiying YANG , Yunlong FU . Zinc metal-organic framework with high-density free carboxyl oxygen functionalized pore walls for targeted electrochemical sensing of paracetamol. Chinese Journal of Inorganic Chemistry, 2024, 40(5): 907-918. doi: 10.11862/CJIC.20230431
9. [9]
  Min WANG , Dehua XIN , Yaning SHI , Wenyao ZHU , Yuanqun ZHANG , Wei ZHANG . Construction and full-spectrum catalytic performance of multilevel Ag/Bi/nitrogen vacancy g-C₃N₄/Ti₃C₂T_x Schottky junction. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1123-1134. doi: 10.11862/CJIC.20230477
10. [10]
  Zhuo WANG , Junshan ZHANG , Shaoyan YANG , Lingyan ZHOU , Yedi LI , Yuanpei LAN . Preparation and photocatalytic performance of CeO₂-reduced graphene oxide by thermal decomposition. Chinese Journal of Inorganic Chemistry, 2024, 40(9): 1708-1718. doi: 10.11862/CJIC.20240067
11. [11]
  Kexin Dong , Chuqi Shen , Ruyu Yan , Yanping Liu , Chunqiang Zhuang , Shijie Li . Integration of Plasmonic Effect and S-Scheme Heterojunction into Ag/Ag₃PO₄/C₃N₅ Photocatalyst for Boosted Photocatalytic Levofloxacin Degradation. Acta Physico-Chimica Sinica, 2024, 40(10): 2310013-. doi: 10.3866/PKU.WHXB202310013
12. [12]
  Youlin SI , Shuquan SUN , Junsong YANG , Zijun BIE , Yan CHEN , Li LUO . Synthesis and adsorption properties of Zn(Ⅱ) metal-organic framework based on 3, 3', 5, 5'-tetraimidazolyl biphenyl ligands. Chinese Journal of Inorganic Chemistry, 2024, 40(9): 1755-1762. doi: 10.11862/CJIC.20240061
13. [13]
  Juntao Yan , Liang Wei . 2D S-Scheme Heterojunction Photocatalyst. Acta Physico-Chimica Sinica, 2024, 40(10): 2312024-. doi: 10.3866/PKU.WHXB202312024
14. [14]
  Xiaosong PU , Hangkai WU , Taohong LI , Huijuan LI , Shouqing LIU , Yuanbo HUANG , Xuemei LI . Adsorption performance and removal mechanism of Cd(Ⅱ) in water by magnesium modified carbon foam. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1537-1548. doi: 10.11862/CJIC.20240030
15. [15]
  Qianqian Liu , Xing Du , Wanfei Li , Wei-Lin Dai , Bo Liu . Synergistic Effects of Internal Electric and Dipole Fields in SnNb₂O₆/Nitrogen-Enriched C₃N₅ S-Scheme Heterojunction for Boosting Photocatalytic Performance. Acta Physico-Chimica Sinica, 2024, 40(10): 2311016-. doi: 10.3866/PKU.WHXB202311016
16. [16]
  Bing LIU , Huang ZHANG , Hongliang HAN , Changwen HU , Yinglei ZHANG . Visible light degradation of methylene blue from water by triangle Au@TiO₂ mesoporous catalyst. Chinese Journal of Inorganic Chemistry, 2024, 40(5): 941-952. doi: 10.11862/CJIC.20230398
17. [17]
  Yi YANG , Shuang WANG , Wendan WANG , Limiao CHEN . Photocatalytic CO₂ reduction performance of Z-scheme Ag-Cu₂O/BiVO₄ photocatalyst. Chinese Journal of Inorganic Chemistry, 2024, 40(5): 895-906. doi: 10.11862/CJIC.20230434
18. [18]
  Yanhui XUE , Shaofei CHAO , Man XU , Qiong WU , Fufa WU , Sufyan Javed Muhammad . Construction of high energy density hexagonal hole MXene aqueous supercapacitor by vacancy defect control strategy. Chinese Journal of Inorganic Chemistry, 2024, 40(9): 1640-1652. doi: 10.11862/CJIC.20240183
19. [19]
  Siyu HOU , Weiyao LI , Jiadong LIU , Fei WANG , Wensi LIU , Jing YANG , Ying ZHANG . Preparation and catalytic performance of magnetic nano iron oxide by oxidation co-precipitation method. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1577-1582. doi: 10.11862/CJIC.20230469
20. [20]
  Kai Han , Guohui Dong , Ishaaq Saeed , Tingting Dong , Chenyang Xiao . Morphology and photocatalytic tetracycline degradation of g-C3N4 optimized by the coal gangue. Chinese Journal of Structural Chemistry, 2024, 43(2): 100208-100208. doi: 10.1016/j.cjsc.2023.100208

Get Citation

PDF

XML

Metrics

PDF Downloads(28)
Abstract views(2043)
HTML views(700)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142