1yfr: Difference between revisions
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New page: left|200px<br /><applet load="1yfr" size="450" color="white" frame="true" align="right" spinBox="true" caption="1yfr, resolution 2.15Å" /> '''crystal structure of... |
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[[Image:1yfr.gif|left|200px]]<br /><applet load="1yfr" size=" | [[Image:1yfr.gif|left|200px]]<br /><applet load="1yfr" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1yfr, resolution 2.15Å" /> | caption="1yfr, resolution 2.15Å" /> | ||
'''crystal structure of alanyl-tRNA synthetase in complex with ATP and magnesium'''<br /> | '''crystal structure of alanyl-tRNA synthetase in complex with ATP and magnesium'''<br /> | ||
==Overview== | ==Overview== | ||
The genetic code is fixed in aminoacylation reactions catalyzed by | The genetic code is fixed in aminoacylation reactions catalyzed by aminoacyl-tRNA synthetases. Amino acid discrimination occurs at two sites: one for amino acid activation and aminoacylation and one for editing misactivated amino acids. Although the active site sieves out bulkier amino acids, misactivation occurs with substrates whose side chains are smaller than the cognate one. Paradoxically, although alanyl-tRNA synthetase activates glycine as well as alanine, the sterically larger (than alanine) serine is also misactivated. Here, we report crystal structures of an active fragment of Aquifex aeolicus alanyl-tRNA synthetase complexed, separately, with Mg2+-ATP, alanine, glycine, and serine. Ala and Gly are bound in similar orientations in a side-chain-accommodating pocket, where alpha-amino and carboxyl groups are stabilized by salt bridges, and the carboxyl by an H-bond from the side chain NH2 of Asn-194. In contrast, whereas the same two salt bridges stabilize bound Ser, H-bonding of the highly conserved (among class II tRNA synthetases) Asn-194 side chain NH2 to the Ser OH, instead of to the carboxyl, forces pocket expansion. Significantly, in the Mg2+-ATP complex, Asn-194 coordinates a Mg2+-alpha-phosphate bridge. Thus, the sieve for Ser exclusion is broken because of selective pressure to retain Asn-194 for Mg2+-ATP and Ala binding. | ||
==About this Structure== | ==About this Structure== | ||
1YFR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] with MG and ATP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] Full crystallographic information is available from [http:// | 1YFR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=ATP:'>ATP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YFR OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Aquifex aeolicus]] | [[Category: Aquifex aeolicus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Schimmel, P | [[Category: Schimmel, P R.]] | ||
[[Category: Swairjo, M | [[Category: Swairjo, M A.]] | ||
[[Category: ATP]] | [[Category: ATP]] | ||
[[Category: MG]] | [[Category: MG]] | ||
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[[Category: magnesium bridge]] | [[Category: magnesium bridge]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:04:56 2008'' | ||
