Sandbox Reserved 1806

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Revision as of 20:13, 27 April 2023

This Sandbox is Reserved from Mar 1 through Jun 1, 2023 for use in the course CHEM 351 Biochemistry taught by Bonnie_Hall at the Grand View University, Des Moines, USA. This reservation includes Sandbox Reserved 1796 through Sandbox Reserved 1811.

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Pyrrolysine (2Q7H) Structure

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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.

1 Function of your protein
2 Biological relevance and broader implications
3 Important amino acids
4 Structural highlights
5 Other important features

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)

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.

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Other important features

References

^[3] ^[4]

↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
↑ Kavran JM, Gundllapalli S, O'Donoghue P, Englert M, Soll D, Steitz TA. Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation. Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11268-73. Epub 2007 Jun 25. PMID:17592110
↑ Nozawa K, O'Donoghue P, Gundllapalli S, Araiso Y, Ishitani R, Umehara T, Soll D, Nureki O. Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality. Nature. 2009 Feb 26;457(7233):1163-7. Epub 2008 Dec 31. PMID:19118381 doi:10.1038/nature07611

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_Reserved_1806"

@@ Line 15: / Line 15: @@
 == Important amino acids==
 <scene name='95/954103/Protein_2q7h/2'>Ligand</scene>, 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 <scene name='95/954103/Ligand_bound/1'>ligand</scene> 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)
 == Structural highlights ==
@@ Line 28: / Line 34: @@
 == References ==
 <ref> PMID:17592110 </ref>
+<ref> PMID:19118381 </ref>
 <references/>

Sandbox Reserved 1806

From Proteopedia

Revision as of 20:13, 27 April 2023

Pyrrolysine (2Q7H) Structure

Contents

Function of your protein

Biological relevance and broader implications

Important amino acids

Structural highlights

Other important features

References

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