3adc: Difference between revisions

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-{{Seed}}
-[[Image:3adc.jpg|left|200px]]
-<!--
+==Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and AMPPNP (crystal type 2)==
-The line below this paragraph, containing "STRUCTURE_3adc", creates the "Structure Box" on the page.
+<StructureSection load='3adc' size='340' side='right'caption='[[3adc]], [[Resolution|resolution]] 2.90&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'>[[3adc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661] and [https://en.wikipedia.org/wiki/Methanopyrus_kandleri Methanopyrus kandleri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ADC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ADC 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]] 2.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_3adc|  PDB=3adc  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3adc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3adc OCA], [https://pdbe.org/3adc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3adc RCSB], [https://www.ebi.ac.uk/pdbsum/3adc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3adc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PSTK_METJA PSTK_METJA] Specifically phosphorylates seryl-tRNA(Sec) to O-phosphoseryl-tRNA(Sec), an activated intermediate for selenocysteine biosynthesis.
+== 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/ad/3adc_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3adc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The 21(st) amino acid, selenocysteine (Sec), is assigned to the codon UGA and is biosynthesized on the selenocysteine-specific tRNA (tRNA(Sec)) with the corresponding anticodon. In archaea/eukarya, tRNA(Sec) is ligated with serine by seryl-tRNA synthetase (SerRS), the seryl moiety is phosphorylated by O-phosphoseryl-tRNA kinase (PSTK), and the phosphate group is replaced with selenol by Sep-tRNA:Sec-tRNA synthase. PSTK selectively phosphorylates seryl-tRNA(Sec), while SerRS serylates both tRNA(Ser) and tRNA(Sec). In this study, we determined the crystal structures of the archaeal tRNA(Sec).PSTK complex. PSTK consists of two independent linker-connected domains, the N-terminal catalytic domain (NTD) and the C-terminal domain (CTD). The D-arm.CTD binding occurs independently of and much more strongly than the acceptor-arm.NTD binding. PSTK thereby distinguishes the characteristic D arm with the maximal stem and the minimal loop of tRNA(Sec) from the canonical D arm of tRNA(Ser), without interacting with the anticodon. This mechanism is essential for the UGA-specific encoding of selenocysteine.
-===Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and AMPPNP (crystal type 2)===
+Structural basis for the major role of O-phosphoseryl-tRNA kinase in the UGA-specific encoding of selenocysteine.,Chiba S, Itoh Y, Sekine S, Yokoyama S Mol Cell. 2010 Aug 13;39(3):410-20. PMID:20705242<ref>PMID:20705242</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3adc" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-ADC is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ADC OCA].
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-[[Category: Methanocaldococcus jannaschii]]
+== References ==
-[[Category: Chiba, S.]]
+<references/>
-[[Category: Itoh, Y.]]
+__TOC__
-[[Category: Sekine, S.]]
+</StructureSection>
-[[Category: Yokoyama, S.]]
+[[Category: Large Structures]]
-[[Category: Atp-binding]]
+[[Category: Methanocaldococcus jannaschii DSM 2661]]
-[[Category: Kinase]]
+[[Category: Methanopyrus kandleri]]
-[[Category: Nucleotide-binding]]
+[[Category: Chiba S]]
-[[Category: Protein-rna complex]]
+[[Category: Itoh Y]]
-[[Category: Transferase]]
+[[Category: Sekine S]]
-[[Category: Transferase-rna complex]]
+[[Category: Yokoyama S]]
-[[Category: Trna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 28 12:35:34 2010''