3foc: Difference between revisions

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-{{Seed}}
-[[Image:3foc.jpg|left|200px]]
-<!--
+==Tryptophanyl-tRNA synthetase from Giardia lamblia==
-The line below this paragraph, containing "STRUCTURE_3foc", creates the "Structure Box" on the page.
+<StructureSection load='3foc' size='340' side='right'caption='[[3foc]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3foc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Giardia_lamblia_ATCC_50803 Giardia lamblia ATCC 50803]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FOC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FOC FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.09&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3foc|  PDB=3foc  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3foc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3foc OCA], [https://pdbe.org/3foc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3foc RCSB], [https://www.ebi.ac.uk/pdbsum/3foc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3foc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A8B8N3_GIAIC A8B8N3_GIAIC]
+== 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/fo/3foc_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=3foc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The 2.1A crystal structure of tryptophanyl-tRNA synthetase (TrpRS) from the diplomonad Giardia lamblia reveals that the N-terminus of this class I aminoacyl-tRNA synthetase forms a 16-residue alpha-helix. This helix replaces a beta-hairpin that is required by human TrpRS for normal activity and has been inferred to play a similar role in all eukaryotic TrpRS. The primary sequences of TrpRS homologs from several basal eukaryotes including Giardia lack a set of three residues observed to stabilize interactions with this beta-hairpin in the human TrpRS. Thus the present structure suggests that the activation reaction mechanism of TrpRS from the basal eukaryote G. lamblia differs from that of higher eukaryotes. Furthermore, the protein as observed in the crystal forms an (alpha(2))(2) homotetramer. The canonical dimer interface observed in all previous structures of tryptophanyl-tRNA synthetases is maintained, but in addition each N-terminal alpha-helix reciprocally interlocks with the equivalent helix from a second dimer to form a dimer of dimers. Although we have no evidence for tetramer formation in vivo, modeling indicates that the crystallographically observed tetrameric structure would be compatible with the tRNA binding mode used by dimeric TrpRS and TyrRS.
-===Tryptophanyl-tRNA synthetase from Giardia lamblia===
+The structure of tryptophanyl-tRNA synthetase from Giardia lamblia reveals divergence from eukaryotic homologs.,Arakaki TL, Carter M, Napuli AJ, Verlinde CL, Fan E, Zucker F, Buckner FS, Van Voorhis WC, Hol WG, Merritt EA J Struct Biol. 2010 Aug;171(2):238-43. Epub 2010 May 8. PMID:20438846<ref>PMID:20438846</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3foc" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16552146}}, adds the Publication Abstract to the page
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16552146 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16552146}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Giardia lamblia ATCC 50803]]
-FOC is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Giardia_lamblia_atcc_50803 Giardia lamblia atcc 50803]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FOC OCA].
+[[Category: Large Structures]]
+[[Category: Arakaki TL]]
-==Reference==
+[[Category: Merritt EA]]
-Optimal description of a protein structure in terms of multiple groups undergoing TLS motion., Painter J, Merritt EA, Acta Crystallogr D Biol Crystallogr. 2006 Apr;62(Pt 4):439-50. Epub 2006, Mar 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16552146 16552146]
-[[Category: Giardia lamblia atcc 50803]]
-[[Category: Tryptophan--tRNA ligase]]
-[[Category: Arakaki, T L.]]
-[[Category: MSGPP, Medical Structural Genomics of Pathogenic Protozoa.]]
-[[Category: Merritt, E A.]]
-[[Category: Aminoacyl-trna synthetase]]
-[[Category: Giardiasis]]
-[[Category: Ligase]]
-[[Category: Medical structural genomics of pathogenic protozoa]]
-[[Category: Msgpp]]
-[[Category: Structural genomic]]
-[[Category: Tryptophanyl-trna synthetase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 14 13:39:27 2009''