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2zvf
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 2zvf is ON HOLD until Paper Publication Authors: Naganuma, M., Sekine, S., Fukunaga, R., Yokoyama, S Description: ''Page seeded by [http://oca.we...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase C-terminal dimerization domain== | |
| + | <StructureSection load='2zvf' size='340' side='right'caption='[[2zvf]], [[Resolution|resolution]] 3.20Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[2zvf]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZVF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZVF FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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 id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ztg|2ztg]]</div></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AF_2255, alaS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=2zvf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvf OCA], [https://pdbe.org/2zvf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zvf RCSB], [https://www.ebi.ac.uk/pdbsum/2zvf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zvf ProSAT], [https://www.topsan.org/Proteins/RSGI/2zvf TOPSAN]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [[https://www.uniprot.org/uniprot/SYA_ARCFU SYA_ARCFU]] 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). Incorrectly charged aminoacyl-tRNA(Ala) is also edited in situ by the editing domain.<ref>PMID:19423669</ref> | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zv/2zvf_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2zvf ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Alanyl-tRNA synthetase (AlaRS) specifically recognizes the major identity determinant, the G3:U70 base pair, in the acceptor stem of tRNA(Ala) by both the tRNA-recognition and editing domains. In this study, we solved the crystal structures of 2 halves of Archaeoglobus fulgidus AlaRS: AlaRS-DeltaC, comprising the aminoacylation, tRNA-recognition, and editing domains, and AlaRS-C, comprising the dimerization domain. The aminoacylation/tRNA-recognition domains contain an insertion incompatible with the class-specific tRNA-binding mode. The editing domain is fixed tightly via hydrophobic interactions to the aminoacylation/tRNA-recognition domains, on the side opposite from that in threonyl-tRNA synthetase. A groove formed between the aminoacylation/tRNA-recognition domains and the editing domain appears to be an alternative tRNA-binding site, which might be used for the aminoacylation and/or editing reactions. Actually, the amino acid residues required for the G3:U70 recognition are mapped in this groove. The dimerization domain consists of helical and globular subdomains. The helical subdomain mediates dimerization by forming a helix-loop-helix zipper. The globular subdomain, which is important for the aminoacylation and editing activities, has a positively-charged face suitable for tRNA binding. | ||
| - | + | Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization.,Naganuma M, Sekine S, Fukunaga R, Yokoyama S Proc Natl Acad Sci U S A. 2009 May 26;106(21):8489-94. Epub 2009 May 7. PMID:19423669<ref>PMID:19423669</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 2zvf" style="background-color:#fffaf0;"></div> | ||
| - | + | ==See Also== | |
| + | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Alanine--tRNA ligase]] | ||
| + | [[Category: Arcfl]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Fukunaga, R]] | ||
| + | [[Category: Naganuma, M]] | ||
| + | [[Category: Structural genomic]] | ||
| + | [[Category: Sekine, S]] | ||
| + | [[Category: Yokoyama, S]] | ||
| + | [[Category: Alanyl-trna synthetase]] | ||
| + | [[Category: Aminoacyl-trna synthetase]] | ||
| + | [[Category: Atp-binding]] | ||
| + | [[Category: C-terminal]] | ||
| + | [[Category: Cytoplasm]] | ||
| + | [[Category: Ligase]] | ||
| + | [[Category: National project on protein structural and functional analyse]] | ||
| + | [[Category: Nppsfa]] | ||
| + | [[Category: Nucleotide-binding]] | ||
| + | [[Category: Oligomerization domain]] | ||
| + | [[Category: Protein biosynthesis]] | ||
| + | [[Category: Rsgi]] | ||
Current revision
Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase C-terminal dimerization domain
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Categories: Alanine--tRNA ligase | Arcfl | Large Structures | Fukunaga, R | Naganuma, M | Structural genomic | Sekine, S | Yokoyama, S | Alanyl-trna synthetase | Aminoacyl-trna synthetase | Atp-binding | C-terminal | Cytoplasm | Ligase | National project on protein structural and functional analyse | Nppsfa | Nucleotide-binding | Oligomerization domain | Protein biosynthesis | Rsgi
