Sandbox Reserved 1806: Difference between revisions
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The Catalytic triad amino acids didn't appear on the crystal structure in Protein Data Bank. | The Catalytic triad amino acids didn't appear on the crystal structure in Protein Data Bank. | ||
Intermolecular forces involved in Pyrrolysine tRNA synthetase are Hydrogen bonding between (Pro 136 to Arg 167) or (Glu 169 to Glu 177). | Intermolecular forces involved in Pyrrolysine tRNA synthetase are <scene name='95/954103/Hydrogen_bonding/1'>Hydrogen</scene> bonding between (Pro 136 to Arg 167) or (Glu 169 to Glu 177). | ||
According to the article, "12 residues that line the amino acid binding pocket and that are generally thought to influence the substrate specificity of PylRS"(pg.9). Most residues in the substrate binding pocket are strictly conserved, however there are 3 amino acids that are considerable and they are: Leucine, Cysteine and Methionine. The positions at which they are located in the enzyme are L309, C348, and M350. | According to the article, "12 residues that line the amino acid binding pocket and that are generally thought to influence the substrate specificity of PylRS"(pg.9). Most residues in the substrate binding pocket are strictly conserved, however there are 3 amino acids that are considerable and they are: <scene name='95/954103/Leucine_amino_acid/1'>Leucine</scene>, <scene name='95/954103/Cysteine_amino_acid/1'>Cysteine</scene> and <scene name='95/954103/Methionine_amino_acid/1'>Methionine</scene>. The positions at which they are located in the enzyme are L309, C348, and M350. | ||
== Structural highlights == | == Structural highlights == | ||
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The <scene name='95/954103/Quaternary_structure/1'>quaternary structure</scene> of a protein is when several protein chains or subunits are packed altogether. Each of the protein chains or subunits have their own primary, secondary, and tertiary structure and are held together by van der Waals forces and hydrogen bonds between nonpolar side chains. | The <scene name='95/954103/Quaternary_structure/1'>quaternary structure</scene> of a protein is when several protein chains or subunits are packed altogether. Each of the protein chains or subunits have their own primary, secondary, and tertiary structure and are held together by van der Waals forces and hydrogen bonds between nonpolar side chains. | ||
A ''space-filling view | A <scene name='95/954103/Space_filling_of_protein/1'>space-filling</scene> view of a protein is a 3-dimensional model that gives a better picture of what the molecule would look and what the overall shape of the protein would be. | ||
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. | This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. | ||
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== Other important features == | == Other important features == | ||
Pyrrolysine tRNA synthetase is able to form a protein dimer. A protein dimer is a macromolecular complex formed by two protein monomers, or single proteins. | Pyrrolysine tRNA synthetase is able to form a protein dimer. A <scene name='95/954103/Secondary_structure/2'>protein dimer</scene> is a macromolecular complex formed by two protein monomers, or single proteins. | ||
Larger structures are important to the proteins function because beginning from the primary structure, the unique sequence of amino acids dictate the 3D conformation the folded protein will have, which will then determine the function of the protein. The tertiary structure of a protein is the most important level because it determines the enzyme activity of a protein. | Larger structures are important to the proteins function because beginning from the primary structure, the unique sequence of amino acids dictate the 3D conformation the folded protein will have, which will then determine the function of the protein. The tertiary structure of a protein is the most important level because it determines the enzyme activity of a protein. | ||
Another important feature of Pyrrolysine tRNA synthetase is that unlike other aminoacyl-tRNA synthetases that are commonly used for genetic code expansion, PylRS does not cross react with other tRNAs in both bacterial and eukaryotic hosts. This is important because the PylRS and tRNA pyl pair can be used to install ncAAs into proteins in a variety of model organisms. Secondly, PylRS has a remarkably high tolerance for structurally disparate ncAA substrates, which is attributed to the large size of the amino acid binding pocket within the enzyme's active site. Finally, unlike most aaRSs, PylRS does not interact with the codon of its cognate tRNA; therefore the anticodon can be mutated to recognize codons other than UAG without impacting tRNA recognition by PylRS. | Another important feature of Pyrrolysine tRNA synthetase is that unlike other aminoacyl-tRNA synthetases that are commonly used for genetic code expansion, PylRS does not cross react with other tRNAs in both bacterial and eukaryotic hosts. This is important because the PylRS and tRNA pyl pair can be used to install ncAAs into proteins in a variety of model organisms. Secondly, PylRS has a remarkably high tolerance for structurally disparate ncAA substrates, which is attributed to the large size of the amino acid binding pocket within the enzyme's active site. Finally, unlike most aaRSs, PylRS does not interact with the codon of its cognate tRNA; therefore the anticodon can be mutated to recognize codons other than UAG without impacting tRNA recognition by PylRS. | ||
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
<ref> PMID:17592110 </ref> | <ref> PMID:17592110 </ref> | ||
<ref> PMID:19118381 </ref> | <ref> PMID:19118381 </ref> | ||
<ref> PMID:36152750 </ref> | |||
<references/> | <references/> | ||
