2e7j

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[[Image:2e7j.jpg|left|200px]]<br /><applet load="2e7j" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2e7j, resolution 2.40&Aring;" />
 
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'''Crystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobus fulgidus'''<br />
 
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==Overview==
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==Crystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobus fulgidus==
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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.
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<StructureSection load='2e7j' size='340' side='right'caption='[[2e7j]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2e7j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E7J FirstGlance]. <br>
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2E7J is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=PLP:'>PLP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E7J OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<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>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e7j OCA], [https://pdbe.org/2e7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e7j RCSB], [https://www.ebi.ac.uk/pdbsum/2e7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e7j ProSAT], [https://www.topsan.org/Proteins/RSGI/2e7j TOPSAN]</span></td></tr>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17512006 17512006]
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e7/2e7j_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2e7j ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Archaeoglobus fulgidus]]
[[Category: Archaeoglobus fulgidus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Fukunaga, R.]]
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[[Category: Fukunaga R]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Yokoyama S]]
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[[Category: Yokoyama, S.]]
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[[Category: PLP]]
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[[Category: SO4]]
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[[Category: lyase]]
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[[Category: national project on protein structural and functional analyses]]
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[[Category: nppsfa]]
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[[Category: riken structural genomics/proteomics initiative]]
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[[Category: rsgi]]
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[[Category: seven-stranded bete-strand]]
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[[Category: structural genomics]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:06:56 2008''
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Current revision

Crystal Structure of Sep-tRNA:Cys-tRNA Synthase from Archaeoglobus fulgidus

PDB ID 2e7j

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