6kqy

From Proteopedia

Crystal structure of human leucyl-tRNA synthetase, Leucine-bound form

PDB ID 6kqy

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Structural highlights

6kqy is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.3Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

SYLC_HUMAN Acute infantile liver failure-multisystemic involvement syndrome. The disease is caused by mutations affecting the gene represented in this entry.

Function

SYLC_HUMAN Catalyzes the specific attachment of an amino acid to its cognate tRNA in a two step reaction: the amino acid (AA) is first activated by ATP to form AA-AMP and then transferred to the acceptor end of the tRNA. Exhibits a post-transfer editing activity to hydrolyze mischarged tRNAs.^[1]

Publication Abstract from PubMed

Leucyl-tRNA synthetase 1 (LARS1) mediates activation of leucine-dependent mechanistic target of rapamycin complex 1 (mTORC1) as well as ligation of leucine to its cognate tRNAs, yet its mechanism of leucine sensing is poorly understood. Here we describe leucine binding-induced conformational changes of LARS1. We determine different crystal structures of LARS1 complexed with leucine, ATP, and a reaction intermediate analog, leucyl-sulfamoyl-adenylate (Leu-AMS), and find two distinct functional states of LARS1 for mTORC1 activation. Upon leucine binding to the synthetic site, H251 and R517 in the connective polypeptide and (50)FPYPY(54) in the catalytic domain change the hydrogen bond network, leading to conformational change in the C-terminal domain, correlating with RagD association. Leucine binding to LARS1 is increased in the presence of ATP, further augmenting leucine-dependent interaction of LARS1 and RagD. Thus, this work unveils the structural basis for leucine-dependent long-range communication between the catalytic and RagD-binding domains of LARS1 for mTORC1 activation.

Leucine-sensing mechanism of leucyl-tRNA synthetase 1 for mTORC1 activation.,Kim S, Yoon I, Son J, Park J, Kim K, Lee JH, Park SY, Kang BS, Han JM, Hwang KY, Kim S Cell Rep. 2021 Apr 27;35(4):109031. doi: 10.1016/j.celrep.2021.109031. PMID:33910001^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Seiradake E, Mao W, Hernandez V, Baker SJ, Plattner JJ, Alley MR, Cusack S. Crystal structures of the human and fungal cytosolic Leucyl-tRNA synthetase editing domains: A structural basis for the rational design of antifungal benzoxaboroles. J Mol Biol. 2009 Jul 10;390(2):196-207. Epub 2009 May 6. PMID:19426743 doi:10.1016/j.jmb.2009.04.073
↑ Kim S, Yoon I, Son J, Park J, Kim K, Lee JH, Park SY, Kang BS, Han JM, Hwang KY, Kim S. Leucine-sensing mechanism of leucyl-tRNA synthetase 1 for mTORC1 activation. Cell Rep. 2021 Apr 27;35(4):109031. doi: 10.1016/j.celrep.2021.109031. PMID:33910001 doi:http://dx.doi.org/10.1016/j.celrep.2021.109031