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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Function of your protein

, its function is to facilitate the cotranslational installation of the 22nd amino acid pyrrolysine. PylRS has emerged as a major route to install nonanonical amino acids into proteins in living cells. The organism that Pyrrolysine is from was identified in a subset of methanogenic archaea. Enzymes that are within this class lack the N-terminal tRNA binding domain that is widely conserved amongst PylRS enzymes, yet they remain active and orthogonal in bacteria and eukaryotes.

Biological relevance and broader implications

Pyrrolysine is important for the organism because it plays a unique role in the key step in the growth of methanogens by activating the methyl group of these substrates for transfer to a corrinoid cofactor. If for whatever reason the tRNA is defective, mistranslation will occur and the amino acid will be attached to the wrong tRNA and misplaced in the protein. Mistranslation can be toxic for bacteria and mammalian cells which could eventually lead to mutations in the organism.

Important amino acids

, A ligand is a small molecule, protein or ion that binds to the DNA double helix. Once it binds to the protein it has the ability to form complexes with other biomolecules in order to perform biological processes. The in this protein is YLY (2R)-2-AMINO-6-({[(2S,3R)-3-METHYLPYRROLIDIN-2-YL]CARBONYL}AMINO)HEXANOYL [(2S,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL HYDROGEN (R)-PHOSPHATE.

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).

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.

Structural highlights

Pyrrolysine has 2 domains, one called the N-terminal and the other being the C-terminal. Pyrrolysine is a modified lysine with a 4-methylpyrroline-5-carboxylate group linked by an amide to the ɛ-amino group. Pyrrolysine is lysine in which has a pyrroline ring linked to the end of the lysine side chain. The tertiary structure of a protein is the overall 3D structure of the protein. The protein is stabilized by outside polar hydrophilic hydrogen and ionic bond interactions, and internal hydrophobic interactions between non-polar amino acid side chains. The quaternary structure 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.

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Other important features