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Theoretical study o...
Theoretical study of the RNA hydrolysis mechanism of the dinuclear zinc enzyme RNase Z
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- Liao, Rong-Zhen (author)
- Stockholms universitet,Institutionen för organisk kemi
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- Himo, Fahmi (author)
- Stockholms universitet,Institutionen för organisk kemi
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Yu, Jian-Guo (author)
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Liu, Ruo-Zhuang (author)
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(creator_code:org_t)
- 2009-06-30
- 2009
- English.
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In: European Journal of Inorganic Chemistry. - Weinheim : Wiley. - 1434-1948 .- 1099-1948 .- 1099-0682. ; :20, s. 2967-2972
- Related links:
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Subject headings
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- RNase Z is a dinuclear zinc enzyme that catalyzes the removal of the tRNA 3'-end trailer. Density functional theory is used to investigate the phosphodiester hydrolysis mechanism of this enzyme with a model of the active site constructed on the basis of the crystal structure. The calculations imply that the reaction proceeds through two steps. The first step is a nucleophihc attack by a bridging hydroxide coupled with protonation of the leaving group by a Glu-His diad. Subsequently, a water molecule activated by the same Glu-His diad makes a reverse attack, regenerating the bridging hydroxide. The second step is calculated to be the rate-limiting step with a barrier of 18 kcal/mol, in good agreement with experimental kinetic studies. Both zinc ions participate in substrate binding and orientation, facilitating nucleophilic attack. In addition, they act as electrophilic catalysts to stabilize the pentacoordinate trigonal-bipyramidal transition states.
Subject headings
- NATURVETENSKAP -- Kemi (hsv//swe)
- NATURAL SCIENCES -- Chemical Sciences (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Andra medicinska och farmaceutiska grundvetenskaper (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Other Basic Medicine (hsv//eng)
Keyword
- Enzyme catalysis
- Metalloenzymes
- Dinuclear zinc enzymes
- Density functional calculations
- Hydrolysis
- Reaction mechanisms
- Zinc
- Chemistry
- Kemi
- Chemistry
Publication and Content Type
- ref (subject category)
- art (subject category)
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