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1yfr

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{{STRUCTURE_1yfr| PDB=1yfr | SCENE= }}
{{STRUCTURE_1yfr| PDB=1yfr | SCENE= }}
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'''crystal structure of alanyl-tRNA synthetase in complex with ATP and magnesium'''
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===crystal structure of alanyl-tRNA synthetase in complex with ATP and magnesium===
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==Overview==
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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.
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The line below this paragraph, {{ABSTRACT_PUBMED_15657145}}, adds the Publication Abstract to the page
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(as it appears on PubMed at http://www.pubmed.gov), where 15657145 is the PubMed ID number.
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{{ABSTRACT_PUBMED_15657145}}
==About this Structure==
==About this Structure==
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==Reference==
==Reference==
Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase., Swairjo MA, Schimmel PR, Proc Natl Acad Sci U S A. 2005 Jan 25;102(4):988-93. Epub 2005 Jan 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15657145 15657145]
Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase., Swairjo MA, Schimmel PR, Proc Natl Acad Sci U S A. 2005 Jan 25;102(4):988-93. Epub 2005 Jan 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15657145 15657145]
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Alanyl-tRNA synthetase crystal structure and design for acceptor-stem recognition., Swairjo MA, Otero FJ, Yang XL, Lovato MA, Skene RJ, McRee DE, Ribas de Pouplana L, Schimmel P, Mol Cell. 2004 Mar 26;13(6):829-41. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15053876 15053876]
[[Category: Alanine--tRNA ligase]]
[[Category: Alanine--tRNA ligase]]
[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
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[[Category: Bent atp conformation]]
[[Category: Bent atp conformation]]
[[Category: Magnesium bridge]]
[[Category: Magnesium bridge]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 16:16:04 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 14:12:15 2008''

Revision as of 11:12, 29 July 2008

Image:1yfr.png

Template:STRUCTURE 1yfr

crystal structure of alanyl-tRNA synthetase in complex with ATP and magnesium

Template:ABSTRACT PUBMED 15657145

About this Structure

1YFR is a Single protein structure of sequence from Aquifex aeolicus. Full crystallographic information is available from OCA.

Reference

Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase., Swairjo MA, Schimmel PR, Proc Natl Acad Sci U S A. 2005 Jan 25;102(4):988-93. Epub 2005 Jan 18. PMID:15657145

Alanyl-tRNA synthetase crystal structure and design for acceptor-stem recognition., Swairjo MA, Otero FJ, Yang XL, Lovato MA, Skene RJ, McRee DE, Ribas de Pouplana L, Schimmel P, Mol Cell. 2004 Mar 26;13(6):829-41. PMID:15053876

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