1riq: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1riq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RIQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RIQ FirstGlance]. <br> | <table><tr><td colspan='2'>[[1riq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RIQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RIQ FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ALAS, AQ_1293 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ALAS, AQ_1293 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</td></tr> | ||
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr> | ||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1riq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1riq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1riq RCSB], [http://www.ebi.ac.uk/pdbsum/1riq PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1riq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1riq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1riq RCSB], [http://www.ebi.ac.uk/pdbsum/1riq PDBsum]</span></td></tr> | ||
<table> | </table> | ||
== Function == | |||
[[http://www.uniprot.org/uniprot/SYA_AQUAE SYA_AQUAE]] Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain (By similarity).[HAMAP-Rule:MF_00036] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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[[Category: Alanine--tRNA ligase]] | [[Category: Alanine--tRNA ligase]] | ||
[[Category: Aquifex aeolicus]] | [[Category: Aquifex aeolicus]] | ||
[[Category: Lovato, M A | [[Category: Lovato, M A]] | ||
[[Category: McRee, D E | [[Category: McRee, D E]] | ||
[[Category: Otero, F J | [[Category: Otero, F J]] | ||
[[Category: Pouplana, L Ribas de | [[Category: Pouplana, L Ribas de]] | ||
[[Category: Schimmel, P | [[Category: Schimmel, P]] | ||
[[Category: Skene, R J | [[Category: Skene, R J]] | ||
[[Category: Swairjo, M A | [[Category: Swairjo, M A]] | ||
[[Category: Yang, X L | [[Category: Yang, X L]] | ||
[[Category: Beta sheet and flanking helice]] | [[Category: Beta sheet and flanking helice]] | ||
[[Category: Class ii aminoacyl-trna synthetase]] | [[Category: Class ii aminoacyl-trna synthetase]] | ||
[[Category: Helix-loop-helix motif]] | [[Category: Helix-loop-helix motif]] | ||
[[Category: Ligase]] | [[Category: Ligase]] | ||
Revision as of 21:28, 24 December 2014
The crystal structure of the catalytic fragment of the alanyl-tRNA synthetaseThe crystal structure of the catalytic fragment of the alanyl-tRNA synthetase
Structural highlights
Function[SYA_AQUAE] Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain (By similarity).[HAMAP-Rule:MF_00036] 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 PubMedEarly work on aminoacylation of alanine-specific tRNA (tRNA(Ala)) by alanyl-tRNA synthetase (AlaRS) gave rise to the concept of an early "second genetic code" imbedded in the acceptor stems of tRNAs. A single conserved and position-specific G:U base pair in the tRNA acceptor stem is the key identity determinant. Further understanding has been limited due to lack of a crystal structure of the enzyme. We determined a 2.14 A crystal structure of the 453 amino acid catalytic fragment of Aquifex aeolicus AlaRS. It contains the catalytic domain characteristic of class II synthetases, a helical domain with a hairpin motif critical for acceptor-stem recognition, and a C-terminal domain of a mixed alpha/beta fold. Docking of tRNA(Ala) on AlaRS shows critical contacts with the three domains, consistent with previous mutagenesis and functional data. It also suggests conformational flexibility within the C domain, which might allow for the positional variation of the key G:U base pair seen in some tRNA(Ala)s. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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