2e7i: Difference between revisions

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-[[Image:2e7i.png|left|200px]]
-{{STRUCTURE_2e7i|  PDB=2e7i  |  SCENE=  }}
+==Crystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobus fulgidus==
+<StructureSection load='2e7i' size='340' side='right'caption='[[2e7i]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2e7i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E7I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E7I FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2e7j|2e7j]]</div></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2e7i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e7i OCA], [https://pdbe.org/2e7i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e7i RCSB], [https://www.ebi.ac.uk/pdbsum/2e7i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e7i ProSAT], [https://www.topsan.org/Proteins/RSGI/2e7i TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/SPSS1_ARCFU SPSS1_ARCFU]] Converts O-phospho-L-seryl-tRNA(Cys) (Sep-tRNA(Cys)) to L-cysteinyl-tRNA(Cys) (Cys-tRNA(Cys)).<ref>PMID:17512006</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/e7/2e7i_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=2e7i ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In the ancient organisms, methanogenic archaea, lacking the canonical cysteinyl-tRNA synthetase, Cys-tRNA(Cys) is produced by an indirect pathway, in which O-phosphoseryl-tRNA synthetase ligates O-phosphoserine (Sep) to tRNA(Cys) and Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep-tRNA(Cys) to Cys-tRNA(Cys). In this study, the crystal structure of SepCysS from Archaeoglobus fulgidus has been determined at 2.4 A resolution. SepCysS forms a dimer, composed of monomers bearing large and small domains. The large domain harbors the seven-stranded beta-sheet, which is typical of the pyridoxal 5'-phosphate (PLP)-dependent enzymes. In the active site, which is located near the dimer interface, PLP is covalently bound to the side-chain of the conserved Lys209. In the proximity of PLP, a sulfate ion is bound by the side-chains of the conserved Arg79, His103, and Tyr104 residues. The active site is located deep within the large, basic cleft to accommodate Sep-tRNA(Cys). On the basis of the surface electrostatic potential, the amino acid residue conservation mapping, the position of the bound sulfate ion, and the substrate amino acid binding manner in other PLP-dependent enzymes, a binding model of Sep-tRNA(Cys) to SepCysS was constructed. One of the three strictly conserved Cys residues (Cys39, Cys42, or Cys247), of one subunit may play a crucial role in the catalysis in the active site of the other subunit.
-===Crystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobus fulgidus===
+Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea: crystal structure of Sep-tRNA:Cys-tRNA synthase from Archaeoglobus fulgidus.,Fukunaga R, Yokoyama S J Mol Biol. 2007 Jun 29;370(1):128-41. Epub 2007 May 4. PMID:17512006<ref>PMID:17512006</ref>
-{{ABSTRACT_PUBMED_17512006}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2e7i" style="background-color:#fffaf0;"></div>
-[[2e7i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E7I OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:017512006</ref><references group="xtra"/>
+</StructureSection>
-[[Category: Archaeoglobus fulgidus]]
+[[Category: Arcfl]]
-[[Category: Fukunaga, R.]]
+[[Category: Large Structures]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Fukunaga, R]]
-[[Category: Yokoyama, S.]]
+[[Category: Structural genomic]]
+[[Category: Yokoyama, S]]
 [[Category: Lyase]]
 [[Category: National project on protein structural and functional analyse]]
 [[Category: Nppsfa]]
-[[Category: Riken structural genomics/proteomics initiative]]
 [[Category: Rsgi]]
 [[Category: Seven-stranded bete-strand]]
-[[Category: Structural genomic]]