1yft: Difference between revisions
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|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=GLY:GLYCINE'>GLY</scene> | |LIGAND= <scene name='pdbligand=GLY:GLYCINE'>GLY</scene> | ||
|ACTIVITY= [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] | |ACTIVITY= <span class='plainlinks'>[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] </span> | ||
|GENE= alaS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus]) | |GENE= alaS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus]) | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1riq|1RIQ]], [[1yfr|1YFR]], [[1yfs|1YFS]], [[1ygb|1YGB]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yft FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yft OCA], [http://www.ebi.ac.uk/pdbsum/1yft PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yft RCSB]</span> | |||
}} | }} | ||
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[[Category: Schimmel, P R.]] | [[Category: Schimmel, P R.]] | ||
[[Category: Swairjo, M A.]] | [[Category: Swairjo, M A.]] | ||
[[Category: alpha-beta fold]] | [[Category: alpha-beta fold]] | ||
[[Category: amino acid binding]] | [[Category: amino acid binding]] | ||
[[Category: helix-loop helix motif]] | [[Category: helix-loop helix motif]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:05:56 2008'' | ||
Revision as of 01:05, 31 March 2008
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| , resolution 2.23Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Gene: | alaS (Aquifex aeolicus) | ||||||
| Activity: | Alanine--tRNA ligase, with EC number 6.1.1.7 | ||||||
| Related: | 1RIQ, 1YFR, 1YFS, 1YGB
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
The crystal structure of the catalytic fragment of alanyl-tRNA synthetase in complex wtih glycine
OverviewOverview
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 StructureAbout this Structure
1YFT is a Single protein structure of sequence from Aquifex aeolicus. Full crystallographic information is available from OCA.
ReferenceReference
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
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