2dq0: Difference between revisions

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-[[Image:2dq0.png|left|200px]]
+==Crystal structure of seryl-tRNA synthetase from Pyrococcus horikoshii complexed with a seryl-adenylate analog==
+<StructureSection load='2dq0' size='340' side='right' caption='[[2dq0]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2dq0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DQ0 FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene><br>
+<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2zr2|2zr2]], [[2zr3|2zr3]]</td></tr>
+<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine--tRNA_ligase Serine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11] </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=2dq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dq0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dq0 RCSB], [http://www.ebi.ac.uk/pdbsum/2dq0 PDBsum], [http://www.topsan.org/Proteins/RSGI/2dq0 TOPSAN]</span></td></tr>
+<table>
+== 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/dq/2dq0_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/chain_selection.php?pdb_ID=2ata ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Seryl-tRNA synthetase (SerRS) catalyzes the ligation of serine to the 3'-end of serine tRNA (tRNA(Ser)), which is typical of the type-2 tRNAs characterized by a long extra arm. The SerRSs are divided into two types, the archaeal/eukaryal and bacterial types. In this study, we solved the crystal structures of the SerRS from the archaeon Pyrococcus horikoshii bound with 5'-O-[N-(L-seryl)-sulfamoyl]-adenosine at 2.6 A and with ATP at 2.8 A, as well as in the apo form at 3.0 A. P. horikoshii SerRS recognizes the seryl and adenylate moieties in a manner similar to those of the bacterial and mitochondrial SerRSs from Thermus thermophilus and Bos taurus, respectively, but different from that of the unusual SerRS from the methanogenic archaeon Methanosarcina barkeri. P. horikoshii SerRS efficiently aminoacylated not only P. horikoshii tRNA(Ser) but also bacterial tRNA(Ser)s from T. thermophilus and Escherichia coli. Models of P. horikoshii SerRS bound with the T. thermophilus and P. horikoshii tRNA(Ser)s suggested that the helical domain of P. horikoshii SerRS is involved in the extra arm binding. This region of P. horikoshii SerRS has additional basic residues as compared with T. thermophilus SerRS, and a Trp residue specific to the archaeal/eukaryal SerRSs. Mutational analyses revealed that the basic and Trp residues are important for tRNA aminoacylation. P. horikoshii SerRS has the archaea-specific insertion, which collaborates with the core domain to form a basic channel leading to the active site. Two sulfate ions are bound to the channel, suggesting that the tRNA 3' region might bind to the channel.
-{{STRUCTURE_2dq0|  PDB=2dq0  |  SCENE=  }}
+Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii.,Itoh Y, Sekine SI, Kuroishi C, Terada T, Shirouzu M, Kuramitsu S, Yokoyama S RNA Biol. 2008 Jul 28;5(3). PMID:18818520<ref>PMID:18818520</ref>
-===Crystal structure of seryl-tRNA synthetase from Pyrococcus horikoshii complexed with a seryl-adenylate analog===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_18818520}}
-==About this Structure==
-[[2dq0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQ0 OCA].
 ==See Also==
 *[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018818520</ref><ref group="xtra">PMID:016962139</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Pyrococcus horikoshii]]
 [[Category: Serine--tRNA ligase]]