Sandbox Reserved 967: Difference between revisions
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== Interactions with nucleic acids == | == Interactions with nucleic acids == | ||
It has been proved that the position of RNA/DNA complex in the active site cleft is determined by several favorable electrostatic interactions between the nucleic acid and positively charged amino acids of the protein<ref name = "ref2">. | It has been proved that the position of RNA/DNA complex in the active site cleft is determined by several favorable electrostatic interactions between the nucleic acid and positively charged amino acids of the protein<ref name = "ref2" />. | ||
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<scene name='60/604486/Site_actif_dna_recongnition/1'>Lysine amino acid in position 128</scene>, 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 ('''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<scene name='60/604486/Site_actif_dna_recongnition/1'>Lysine amino acid in position 128</scene>, 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 ('''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. | ||
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== References == | == References == | ||
</ | <references/> | ||
== Proteopedia page contributors and editors == | == Proteopedia page contributors and editors == | ||
Anaïs Bourbigot & Valériane Keïta | Anaïs Bourbigot & Valériane Keïta | ||
