1riq

From Proteopedia

(Difference between revisions)

Revision as of 08:15, 28 February 2018

The crystal structure of the catalytic fragment of the alanyl-tRNA synthetase

Structural highlights

1riq is a 1 chain structure with sequence from "aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Gene:	ALAS, AQ_1293 ("Aquifex aeolicus" Huber and Stetter 2001)
Activity:	Alanine--tRNA ligase, with EC number 6.1.1.7
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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 PubMed

Early 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.

References

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1riq"

@@ Line 1: / Line 1: @@
 ==The crystal structure of the catalytic fragment of the alanyl-tRNA synthetase==
 <StructureSection load='1riq' size='340' side='right' caption='[[1riq]], [[Resolution|resolution]] 2.14&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <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" Huber and Stetter 2001])</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 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://pdbe.org/1riq PDBe], [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://pdbe.org/1riq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1riq RCSB], [http://www.ebi.ac.uk/pdbsum/1riq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1riq ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ri/1riq_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ri/1riq_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1riq

From Proteopedia

Revision as of 08:15, 28 February 2018

The crystal structure of the catalytic fragment of the alanyl-tRNA synthetase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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