2e7i: Difference between revisions
New page: left|200px<br /><applet load="2e7i" size="350" color="white" frame="true" align="right" spinBox="true" caption="2e7i, resolution 3.00Å" /> '''Crystal Structure of... |
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== | ==Crystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobus fulgidus== | ||
In the ancient organisms, methanogenic archaea, lacking the canonical | <StructureSection load='2e7i' size='340' side='right'caption='[[2e7i]], [[Resolution|resolution]] 3.00Å' 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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 2e7i" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: Fukunaga, R | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: Yokoyama, S | </StructureSection> | ||
[[Category: | [[Category: Arcfl]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Fukunaga, R]] | |||
[[Category: Structural genomic]] | |||
[[Category: Yokoyama, S]] | |||
[[Category: | [[Category: Lyase]] | ||
[[Category: | [[Category: National project on protein structural and functional analyse]] | ||
[[Category: | [[Category: Nppsfa]] | ||
[[Category: Rsgi]] | |||
[[Category: Seven-stranded bete-strand]] | |||
