4ycu

From Proteopedia

Crystal structure of cladosporin in complex with human lysyl-tRNA synthetase

PDB ID 4ycu

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Structural highlights

4ycu is a 3 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

SYK_HUMAN Defects in KARS are the cause of Charcot-Marie-Tooth disease recessive intermediate type B (CMTRIB) [MIM:613641; also called Charcot-Marie-Tooth neuropathy recessive intermediate B. CMTRIB is a form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Recessive intermediate forms of Charcot-Marie-Tooth disease are characterized by clinical and pathologic features intermediate between demyelinating and axonal peripheral neuropathies, and motor median nerve conduction velocities ranging from 25 to 45 m/sec.^[1]

Function

SYK_HUMAN Catalyzes the specific attachment of an amino acid to its cognate tRNA in a 2 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. When secreted, acts as a signaling molecule that induces immune response through the activation of monocyte/macrophages. Catalyzes the synthesis of diadenosine oligophosphate (Ap4A), a signaling molecule involved in the activation of MITF transcriptional activity. Interacts with HIV-1 virus GAG protein, facilitating the selective packaging of tRNA(3)(Lys), the primer for reverse transcription initiation.^[2] ^[3]

Publication Abstract from PubMed

Pharmaceutical inhibitors of aminoacyl-tRNA synthetases demand high species and family specificity. The antimalarial ATP-mimetic cladosporin selectively inhibits Plasmodium falciparum LysRS (PfLysRS). How the binding to a universal ATP site achieves the specificity is unknown. Here we report three crystal structures of cladosporin with human LysRS, PfLysRS, and a Pf-like human LysRS mutant. In all three structures, cladosporin occupies the class defining ATP-binding pocket, replacing the adenosine portion of ATP. Three residues holding the methyltetrahydropyran moiety of cladosporin are critical for the specificity of cladosporin against LysRS over other class II tRNA synthetase families. The species-exclusive inhibition of PfLysRS is linked to a structural divergence beyond the active site that mounts a lysine-specific stabilizing response to binding cladosporin. These analyses reveal that inherent divergence of tRNA synthetase structural assembly may allow for highly specific inhibition even through the otherwise universal substrate binding pocket and highlight the potential for structure-driven drug development.

Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor.,Fang P, Han H, Wang J, Chen K, Chen X, Guo M Chem Biol. 2015 Jun 18;22(6):734-44. doi: 10.1016/j.chembiol.2015.05.007. Epub, 2015 Jun 11. PMID:26074468^[4]

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

References

↑ McLaughlin HM, Sakaguchi R, Liu C, Igarashi T, Pehlivan D, Chu K, Iyer R, Cruz P, Cherukuri PF, Hansen NF, Mullikin JC, Biesecker LG, Wilson TE, Ionasescu V, Nicholson G, Searby C, Talbot K, Vance JM, Zuchner S, Szigeti K, Lupski JR, Hou YM, Green ED, Antonellis A. Compound heterozygosity for loss-of-function lysyl-tRNA synthetase mutations in a patient with peripheral neuropathy. Am J Hum Genet. 2010 Oct 8;87(4):560-6. doi: 10.1016/j.ajhg.2010.09.008. PMID:20920668 doi:10.1016/j.ajhg.2010.09.008
↑ Zamecnik PC, Stephenson ML, Janeway CM, Randerath K. Enzymatic synthesis of diadenosine tetraphosphate and diadenosine triphosphate with a purified lysyl-sRNA synthetase. Biochem Biophys Res Commun. 1966 Jul 6;24(1):91-7. PMID:5338216
↑ Park SG, Kim HJ, Min YH, Choi EC, Shin YK, Park BJ, Lee SW, Kim S. Human lysyl-tRNA synthetase is secreted to trigger proinflammatory response. Proc Natl Acad Sci U S A. 2005 May 3;102(18):6356-61. Epub 2005 Apr 25. PMID:15851690 doi:10.1073/pnas.0500226102
↑ Fang P, Han H, Wang J, Chen K, Chen X, Guo M. Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor. Chem Biol. 2015 Jun 18;22(6):734-44. doi: 10.1016/j.chembiol.2015.05.007. Epub, 2015 Jun 11. PMID:26074468 doi:http://dx.doi.org/10.1016/j.chembiol.2015.05.007