Sandbox Reserved 434
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===Binding Interactions=== | ===Binding Interactions=== | ||
<scene name='Sandbox_Reserved_434/Scissile_bond_25/4'>The green is residue number 25</scene> | <scene name='Sandbox_Reserved_434/Scissile_bond_25/4'>The green is residue number 25</scene> | ||
| - | + | BINDING INTERACTIONS | |
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| + | Pb2+ in leadzyme cleaves the RNA by cleaving the substrate’s backbone and producing a 2’,3’-cyclic phosphodiester and a 5’-hydroxyl. This first step is common among many ribozymes, however, the 2’,3’-cyclic phosphodiester is hydrolyzed to produce a 3’-phosphodiester. | ||
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| + | Leadzyme requires Pb2+ to cleave RNA and is inhibited by Mg2+, through competitive inhibition. A possible suggestion for Mg2+ inhibition may have to do with the Mg(H2O)6 which bind in the major groove at the G39, G30 and A29 nucleotides at one location (SITE I, in both the ground state and pre-catalytic state), at the U47, G20, and G19 nucleotides from another location (SITE II, from both states), and at the U41, G42, G43, G24, and A25 nucleotides in the ground state (SITE III). This last interaction is particularly important since it “ligates” the trinucleotide bulge, which inhibits the activity of the leadzyme. Since this type of interaction occurs only in the ground state, it is thought to stabilize the ground state and thus prevent catalysis of RNA cleavage. There are some differences in the types of binding involved sites II than in sites I & III. For example. In site II, O6 at the G43 nucleotide shares an H2O with O6 of G42 rather than hydrogen bonding with a separate water molecule. | ||
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| + | Another ion of interest is Sr2+, which binds similarly as Pb2+ but has different catalytic effects due to electronic differences. Similar bonding occurs because of similar ionic radii (Sr2+=1.12A; Pb2+=1.13A). Although there are 3 major Sr2+ binding sites, one particularly important site interacts with G24, G23, and A45, which are located in the Scissile Bond region. This bonding dramatically changes the conformation of the phosphodiester backbone (in the presence of Mg2+ and Sr2). | ||
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| + | Because of such interactions, leadzyme in the presence of only Sr2+ does not show significant cleavage, where leadzyme in the presence of Sr2+ and Pb2+ shows reduced cleavage in comparison to leadzyme and only Pb2+. | ||
===Additional Features=== | ===Additional Features=== | ||
Revision as of 22:47, 22 April 2012
| This Sandbox is Reserved from January 19, 2016, through August 31, 2016 for use for Proteopedia Team Projects by the class Chemistry 423 Biochemistry for Chemists taught by Lynmarie K Thompson at University of Massachusetts Amherst, USA. This reservation includes Sandbox Reserved 425 through Sandbox Reserved 439. |
Contents |
Leadzyme, 1nuv
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Introduction
Leadzyme is a ribozyme, created in vitro through artificial selection. In the presence of lead, leadzyme will bind and cut RNA.
Overall Structure
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Leadzyme is made up of
each shown in a different color. One of the RNA duplexes is shown with nucleotides 18-30 shown in orange and nucleotides 39-49 shown in blue. The duplex contains two The C23 to A45 is shown in black and A25 to G44 is shown in blue.
Binding Interactions
BINDING INTERACTIONS
Pb2+ in leadzyme cleaves the RNA by cleaving the substrate’s backbone and producing a 2’,3’-cyclic phosphodiester and a 5’-hydroxyl. This first step is common among many ribozymes, however, the 2’,3’-cyclic phosphodiester is hydrolyzed to produce a 3’-phosphodiester.
Leadzyme requires Pb2+ to cleave RNA and is inhibited by Mg2+, through competitive inhibition. A possible suggestion for Mg2+ inhibition may have to do with the Mg(H2O)6 which bind in the major groove at the G39, G30 and A29 nucleotides at one location (SITE I, in both the ground state and pre-catalytic state), at the U47, G20, and G19 nucleotides from another location (SITE II, from both states), and at the U41, G42, G43, G24, and A25 nucleotides in the ground state (SITE III). This last interaction is particularly important since it “ligates” the trinucleotide bulge, which inhibits the activity of the leadzyme. Since this type of interaction occurs only in the ground state, it is thought to stabilize the ground state and thus prevent catalysis of RNA cleavage. There are some differences in the types of binding involved sites II than in sites I & III. For example. In site II, O6 at the G43 nucleotide shares an H2O with O6 of G42 rather than hydrogen bonding with a separate water molecule.
Another ion of interest is Sr2+, which binds similarly as Pb2+ but has different catalytic effects due to electronic differences. Similar bonding occurs because of similar ionic radii (Sr2+=1.12A; Pb2+=1.13A). Although there are 3 major Sr2+ binding sites, one particularly important site interacts with G24, G23, and A45, which are located in the Scissile Bond region. This bonding dramatically changes the conformation of the phosphodiester backbone (in the presence of Mg2+ and Sr2).
Because of such interactions, leadzyme in the presence of only Sr2+ does not show significant cleavage, where leadzyme in the presence of Sr2+ and Pb2+ shows reduced cleavage in comparison to leadzyme and only Pb2+.
Additional Features
The is dependent on the inclusion of lead for catalytic effect: no other ion gives the same result.
The addition of lanthanide ions has been found to increase the rate of substrate cleavage.
Studies show that equimolar solutions of neodymium (III) and lead (II) maximize this effect, suggesting that neodymium acts in concert with lead, as an acid catalyst. The site at which the RNA is cleaved remains unchanged.
Credits
Introduction - Jeffrey Salemi
Overall Structure - Adam Ramey
Binding Interactions- Nicholas Vecchiarello
Additional Features - Tom Foley
Fill in your names please. Prof T
