Sandbox Reserved 967: Difference between revisions

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The β6-α6 loop of the H2A protein could play a role in substrate recognition: the minor groove of the double helix molecule straddles this area of the protein, which results in a non-sequence specific cleavage by the enzyme. Moreover, the β6-α6 loop contains a Lysine amino acid in position 128, which might act as a sensor for the hybrid by forming an interaction with the 2’-hydroxyl group of the ribose in the 3’ nucleotide of the RNA primer in the RNA-DNA hybrid<ref name="ref5" /> ('''Figure 2'''). Therefore, since DNA does not contain a 2’-hydroxyl group in it nucleotide sequence, the RNase H2 can only recognize RNA in the hybrid: only ribonucleotides of the RNA strand are positioned in the active site. The RNA-DNA hybrid is placed such that the target phosphodiester bond between the RNA and DNA parts of the hybrid is in the proper orientation for nucleophile attack by a two-metal ion mechanism.

It is important to notice that the Mammalian RNase H2 contains only one cleft with the active site for substrate binding: RNase H2 may recognize single ribonucleotide within a DNA duplex that have a B-form helical structure, as well as longer RNA in RNA-DNA hybrid which adopts intermediate A/B form structure. Thus, the RNase H2 enzyme needs to bind both conformations to able to fully complete all its roles.

It is important to notice that the Mammalian RNase H2 contains only one cleft with the active site for substrate binding: RNase H2 may recognize single ribonucleotide within a DNA duplex that have a B-form helical structure, as well as longer RNA in RNA-DNA hybrid which adopts intermediate A/B form structure<ref name="ref9" />. Thus, the RNase H2 enzyme needs to bind both conformations to able to fully complete all its roles.

Sandbox Reserved 967: Difference between revisions

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Revision as of 17:14, 8 January 2015 view source Valeriane Keita (talk \| contribs) 83 edits No edit summary ← Older edit		Revision as of 17:15, 8 January 2015 view source Valeriane Keita (talk \| contribs) 83 edits No edit summary Newer edit →
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	The β6-α6 loop of the H2A protein could play a role in substrate recognition: the minor groove of the double helix molecule straddles this area of the protein, which results in a non-sequence specific cleavage by the enzyme. Moreover, the β6-α6 loop contains a Lysine amino acid in position 128, which might act as a sensor for the hybrid by forming an interaction with the 2’-hydroxyl group of the ribose in the 3’ nucleotide of the RNA primer in the RNA-DNA hybrid<ref name="ref5" /> ('''Figure 2'''). Therefore, since DNA does not contain a 2’-hydroxyl group in it nucleotide sequence, the RNase H2 can only recognize RNA in the hybrid: only ribonucleotides of the RNA strand are positioned in the active site. The RNA-DNA hybrid is placed such that the target phosphodiester bond between the RNA and DNA parts of the hybrid is in the proper orientation for nucleophile attack by a two-metal ion mechanism.		The β6-α6 loop of the H2A protein could play a role in substrate recognition: the minor groove of the double helix molecule straddles this area of the protein, which results in a non-sequence specific cleavage by the enzyme. Moreover, the β6-α6 loop contains a Lysine amino acid in position 128, which might act as a sensor for the hybrid by forming an interaction with the 2’-hydroxyl group of the ribose in the 3’ nucleotide of the RNA primer in the RNA-DNA hybrid<ref name="ref5" /> ('''Figure 2'''). Therefore, since DNA does not contain a 2’-hydroxyl group in it nucleotide sequence, the RNase H2 can only recognize RNA in the hybrid: only ribonucleotides of the RNA strand are positioned in the active site. The RNA-DNA hybrid is placed such that the target phosphodiester bond between the RNA and DNA parts of the hybrid is in the proper orientation for nucleophile attack by a two-metal ion mechanism.
	It is important to notice that the Mammalian RNase H2 contains only one cleft with the active site for substrate binding: RNase H2 may recognize single ribonucleotide within a DNA duplex that have a B-form helical structure, as well as longer RNA in RNA-DNA hybrid which adopts intermediate A/B form structure. Thus, the RNase H2 enzyme needs to bind both conformations to able to fully complete all its roles.		It is important to notice that the Mammalian RNase H2 contains only one cleft with the active site for substrate binding: RNase H2 may recognize single ribonucleotide within a DNA duplex that have a B-form helical structure, as well as longer RNA in RNA-DNA hybrid which adopts intermediate A/B form structure<ref name="ref9" />. Thus, the RNase H2 enzyme needs to bind both conformations to able to fully complete all its roles.