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This Sandbox is Reserved from September 14, 2021, through May 31, 2022, for use in the class Introduction to Biochemistry taught by User:John Means at the University of Rio Grande, Rio Grande, OH, USA. This reservation includes 5 reserved sandboxes (Sandbox Reserved 1590 through Sandbox Reserved 1594).

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Lysyl-tRNA Synthetase(1BBU)

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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
2 Disease
3 Relevance
4 Structural highlights

Function

Lysyl-tRNA synthetase (LysS) is a member of the class II aminoacyl-tRNA synthetases and catalyses the specific aminoacylation of tRNA(Lys). There are two different proteins that code for lysyl-tRNA synthase, LysS and LysU. The LysS is expressed under normal contionds, where the LysU is overexpressed in conditions like high temperature, anaerobiosis, low external pH, or the presence of leucine. ^[3] The source organism comes from Escherichia coli. The LysS is a protein that plays an important role in the translation of the genetic sequence. The LysS aids in an accurate translation of the mRNA. ^[4]

Disease

A mutation in the LysS has shown to have played a role in the reduction of the outer membrane vesiculation. ^[5]

Relevance

A defect in the translation of the genetic material from LysS would impact the functionality of the protein. The LysS gene has been determined to coincide with the HerC gene. Lysyl-tRNA synthase has been thought to be used for a drug target that lead to drug discovery capable of clearing parasites from mouse models with malaria and cryptosporidiosis infection. ^[6]

Structural highlights

The first interaction that leads to a reorganization of the active site is from the binding of the α amino group from the lysine and the carbonyl oxygen of Gly216. The second interaction is between the carboxylate group and the side chin of Arg262. The interactions of both lead to the . When reorganizing the active sites, the ordering of two loops (residues 215-217 and 444-455) are formed. The change in the conformation of residues 393-409 is another result from the reorganization. The final change is the rotation of a 4-helix bundle (located between motif 2 & 3) by 10°. The results of these interactions is the closing up of active site upon lysine binding.^[7]

References

↑ 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
↑ Onesti S, Desogus G, Brevet A, Chen J, Plateau P, Blanquet S, Brick P. Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding. Biochemistry. 2000 Oct 24;39(42):12853-61. PMID:11041850
↑ Ravishankar S, Ambady A, Swetha RG, Anbarasu A, Ramaiah S, Sambandamurthy VK. Essentiality Assessment of Cysteinyl and Lysyl-tRNA Synthetases of Mycobacterium smegmatis. PLoS One. 2016 Jan 21;11(1):e0147188. doi: 10.1371/journal.pone.0147188., eCollection 2016. PMID:26794499 doi:http://dx.doi.org/10.1371/journal.pone.0147188
↑ Rudd KE. EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res. 2000 Jan 1;28(1):60-4. doi: 10.1093/nar/28.1.60. PMID:10592181 doi:http://dx.doi.org/10.1093/nar/28.1.60
↑ . PMID:1814685116
↑ Onesti S, Desogus G, Brevet A, Chen J, Plateau P, Blanquet S, Brick P. Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding. Biochemistry. 2000 Oct 24;39(42):12853-61. PMID:11041850

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From Proteopedia

Lysyl-tRNA Synthetase(1BBU)

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Function

Disease

Relevance

Structural highlights

References

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