3bcb: Difference between revisions

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-{{Seed}}
-[[Image:3bcb.png|left|200px]]
-<!--
+==Crystal structure of mouse selenocysteine synthase, sodium phosphate soak==
-The line below this paragraph, containing "STRUCTURE_3bcb", creates the "Structure Box" on the page.
+<StructureSection load='3bcb' size='340' side='right'caption='[[3bcb]], [[Resolution|resolution]] 1.85&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'>[[3bcb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BCB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BCB 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]] 1.85&#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=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_3bcb|  PDB=3bcb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bcb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bcb OCA], [https://pdbe.org/3bcb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bcb RCSB], [https://www.ebi.ac.uk/pdbsum/3bcb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bcb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SPCS_MOUSE SPCS_MOUSE] Converts O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis (By similarity).
+== 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/bc/3bcb_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=3bcb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In eukaryotes and Archaea, selenocysteine synthase (SecS) converts O-phospho-L-seryl-tRNA [Ser]Sec into selenocysteyl-tRNA [Ser]Sec using selenophosphate as the selenium donor compound. The molecular mechanisms underlying SecS activity are presently unknown. We have delineated a 450-residue core of mouse SecS, which retained full selenocysteyl-tRNA [Ser]Sec synthesis activity, and determined its crystal structure at 1.65 A resolution. SecS exhibits three domains that place it in the fold type I family of pyridoxal phosphate (PLP)-dependent enzymes. Two SecS monomers interact intimately and together build up two identical active sites around PLP in a Schiff-base linkage with lysine 284. Two SecS dimers further associate to form a homotetramer. The N terminus, which mediates tetramer formation, and a large insertion that remodels the active site set SecS aside from other members of the family. The active site insertion contributes to PLP binding and positions a glutamate next to the PLP, where it could repel substrates with a free alpha-carboxyl group, suggesting why SecS does not act on free O-phospho-l-serine. Upon soaking crystals in phosphate buffer, a previously disordered loop within the active site insertion contracted to form a phosphate binding site. Residues that are strictly conserved in SecS orthologs but variant in related enzymes coordinate the phosphate and upon mutation corrupt SecS activity. Modeling suggested that the phosphate loop accommodates the gamma-phosphate moiety of O-phospho-l-seryl-tRNA [Ser]Sec and, after phosphate elimination, binds selenophosphate to initiate attack on the proposed aminoacrylyl-tRNA [Ser]Sec intermediate. Based on these results and on the activity profiles of mechanism-based inhibitors, we offer a detailed reaction mechanism for the enzyme.
-===Crystal structure of mouse selenocysteine synthase, sodium phosphate soak===
+Structure and catalytic mechanism of eukaryotic selenocysteine synthase.,Ganichkin OM, Xu XM, Carlson BA, Mix H, Hatfield DL, Gladyshev VN, Wahl MC J Biol Chem. 2008 Feb 29;283(9):5849-65. Epub 2007 Dec 19. PMID:18093968<ref>PMID:18093968</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3bcb" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18093968}}, adds the Publication Abstract to the page
+*[[Selenocysteine synthase|Selenocysteine synthase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18093968 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18093968}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-BCB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BCB OCA].
-==Reference==
-Structure and catalytic mechanism of eukaryotic selenocysteine synthase., Ganichkin OM, Xu XM, Carlson BA, Mix H, Hatfield DL, Gladyshev VN, Wahl MC, J Biol Chem. 2008 Feb 29;283(9):5849-65. Epub 2007 Dec 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18093968 18093968]
 [[Category: Mus musculus]]
-[[Category: Single protein]]
+[[Category: Ganichkin OM]]
-[[Category: Ganichkin, O M.]]
+[[Category: Wahl MC]]
-[[Category: Wahl, M C.]]
-[[Category: Crystal structure]]
-[[Category: Cytoplasm]]
-[[Category: Disorder-order transition]]
-[[Category: Phosphate-loop]]
-[[Category: Protein biosynthesis]]
-[[Category: Pyridoxal phosphate]]
-[[Category: Selenium]]
-[[Category: Transferase]]
-[[Category: X-ray crystallography]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 12:02:53 2008''