3nel

From Proteopedia

Aspartyl-tRNA synthetase complexed with aspartic acid

PDB ID 3nel

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Structural highlights

3nel is a 2 chain structure with sequence from Thermococcus kodakarensis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.954Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SYD_THEKO Catalyzes the attachment of L-aspartate to tRNA(Asp) in a two-step reaction: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp). Is specific for tRNA(Asp) since it aspartylates tRNA(Asn) 3 orders of magnitude less efficiently than tRNA(Asp).^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The crystal structure of aspartyl-tRNA synthetase (AspRS) from Pyrococcus kodakaraensis was solved at 1.9 A resolution. The sequence and three-dimensional structure of the catalytic domain are highly homologous to those of eukaryotic AspRSs. In contrast, the N-terminal domain, whose function is to bind the tRNA anticodon, is more similar to that of eubacterial enzymes. Its structure explains the unique property of archaeal AspRSs of accommodating both tRNAAsp and tRNAAsn. Soaking the apo-enzyme crystals with ATP and aspartic acid both separately and together allows the adenylate formation to be followed. Due to the asymmetry of the dimeric enzyme in the crystalline state, different steps of the reaction could be visualized within the same crystal. Four different states of the aspartic acid activation reaction could thus be characterized, revealing the functional correlation of the observed conformational changes. The binding of the amino acid substrate induces movement of two invariant loops which secure the position of the peptidyl moiety for adenylate formation. An unambiguous spatial and functional assignment of three magnesium ion cofactors can be made. This study shows the important role of residues present in both archaeal and eukaryotic AspRSs, but absent from the eubacterial enzymes.

Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation.,Schmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry JC, Moras D EMBO J. 1998 Sep 1;17(17):5227-37. PMID:9724658^[4]

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

References

↑ Tumbula-Hansen D, Feng L, Toogood H, Stetter KO, Söll D. Evolutionary divergence of the archaeal aspartyl-tRNA synthetases into discriminating and nondiscriminating forms. J Biol Chem. 2002 Oct 4;277(40):37184-90. PMID:12149259 doi:10.1074/jbc.M204767200
↑ Charron C, Roy H, Blaise M, Giege R, Kern D. Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain. EMBO J. 2003 Apr 1;22(7):1632-43. PMID:12660169 doi:10.1093/emboj/cdg148
↑ Feng L, Tumbula-Hansen D, Toogood H, Soll D. Expanding tRNA recognition of a tRNA synthetase by a single amino acid change. Proc Natl Acad Sci U S A. 2003 May 13;100(10):5676-81. PMID:12730374 doi:10.1073/pnas.0631525100
↑ Schmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry JC, Moras D. Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. EMBO J. 1998 Sep 1;17(17):5227-37. PMID:9724658 doi:10.1093/emboj/17.17.5227