2cj9: Difference between revisions

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-{{Seed}}
-[[Image:2cj9.png|left|200px]]
-<!--
+==Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with an analog of seryladenylate==
-The line below this paragraph, containing "STRUCTURE_2cj9", creates the "Structure Box" on the page.
+<StructureSection load='2cj9' size='340' side='right'caption='[[2cj9]], [[Resolution|resolution]] 2.30&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'>[[2cj9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_barkeri_str._Fusaro Methanosarcina barkeri str. Fusaro]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CJ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CJ9 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]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SSA:5-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE'>SSA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2cj9|  PDB=2cj9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cj9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cj9 OCA], [https://pdbe.org/2cj9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cj9 RCSB], [https://www.ebi.ac.uk/pdbsum/2cj9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cj9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYS2_METBF SYS2_METBF] Catalyzes the attachment of serine to tRNA(Ser). Is also probably able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).<ref>PMID:15364939</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/cj/2cj9_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=2cj9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Methanogenic archaea possess unusual seryl-tRNA synthetase (SerRS), evolutionarily distinct from the SerRSs found in other archaea, eucaryotes and bacteria. The two types of SerRSs show only minimal sequence similarity, primarily within class II conserved motifs 1, 2 and 3. Here, we report a 2.5 A resolution crystal structure of the atypical methanogenic Methanosarcina barkeri SerRS and its complexes with ATP, serine and the nonhydrolysable seryl-adenylate analogue 5'-O-(N-serylsulfamoyl)adenosine. The structures reveal two idiosyncratic features of methanogenic SerRSs: a novel N-terminal tRNA-binding domain and an active site zinc ion. The tetra-coordinated Zn2+ ion is bound to three conserved protein ligands (Cys306, Glu355 and Cys461) and binds the amino group of the serine substrate. The absolute requirement of the metal ion for enzymatic activity was confirmed by mutational analysis of the direct zinc ion ligands. This zinc-dependent serine recognition mechanism differs fundamentally from the one employed by the bacterial-type SerRSs. Consequently, SerRS represents the only known aminoacyl-tRNA synthetase system that evolved two distinct mechanisms for the recognition of the same amino-acid substrate.
-===CRYSTAL STRUCTURE OF METHANOSARCINA BARKERI SERYL-TRNA SYNTHETASE COMPLEXED WITH AN ANALOG OF SERYLADENYLATE===
+Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition.,Bilokapic S, Maier T, Ahel D, Gruic-Sovulj I, Soll D, Weygand-Durasevic I, Ban N EMBO J. 2006 Jun 7;25(11):2498-509. Epub 2006 May 4. PMID:16675947<ref>PMID:16675947</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2cj9" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16675947}}, 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 16675947 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16675947}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-CJ9 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Methanosarcina_barkeri Methanosarcina barkeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CJ9 OCA].
+[[Category: Methanosarcina barkeri str. Fusaro]]
+[[Category: Ahel D]]
-==Reference==
+[[Category: Ban N]]
-<ref group="xtra">PMID:16675947</ref><references group="xtra"/>
+[[Category: Bilokapic S]]
-[[Category: Methanosarcina barkeri]]
+[[Category: Gruic-Sovulj I]]
-[[Category: Serine--tRNA ligase]]
+[[Category: Maier T]]
-[[Category: Ahel, D.]]
+[[Category: Soll D]]
-[[Category: Ban, N.]]
+[[Category: Weygand-Durasevic I]]
-[[Category: Bilokapic, S.]]
-[[Category: Gruic-Sovulj, I.]]
-[[Category: Maier, T.]]
-[[Category: Soll, D.]]
-[[Category: Weygand-Durasevic, I.]]
-[[Category: Ligase]]
-[[Category: Seryladenylate]]
-[[Category: Trna synthetase]]
-[[Category: Zinc ion]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 09:29:26 2009''