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| | ==Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) selenium transferase (SepSecS)== | | ==Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) selenium transferase (SepSecS)== |
| - | <StructureSection load='2z67' size='340' side='right' caption='[[2z67]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='2z67' size='340' side='right'caption='[[2z67]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2z67]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Metmp Metmp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z67 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z67 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2z67]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanococcus_maripaludis_S2 Methanococcus maripaludis S2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z67 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z67 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">spcS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=267377 METMP])</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=2z67 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z67 OCA], [https://pdbe.org/2z67 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z67 RCSB], [https://www.ebi.ac.uk/pdbsum/2z67 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z67 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z67 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z67 OCA], [http://pdbe.org/2z67 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z67 RCSB], [http://www.ebi.ac.uk/pdbsum/2z67 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z67 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SPCS_METMP SPCS_METMP]] Converts O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis.<ref>PMID:17142313</ref> | + | [https://www.uniprot.org/uniprot/SPCS_METMP SPCS_METMP] Converts O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis.<ref>PMID:17142313</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z6/2z67_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z6/2z67_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Metmp]] | + | [[Category: Large Structures]] |
| - | [[Category: Araiso, Y]] | + | [[Category: Methanococcus maripaludis S2]] |
| - | [[Category: Domae, N]] | + | [[Category: Araiso Y]] |
| - | [[Category: Ishitani, R]] | + | [[Category: Domae N]] |
| - | [[Category: Nureki, O]] | + | [[Category: Ishitani R]] |
| - | [[Category: Oshikane, H]] | + | [[Category: Nureki O]] |
| - | [[Category: Pailouer, S]] | + | [[Category: Oshikane H]] |
| - | [[Category: Soll, D]] | + | [[Category: Pailouer S]] |
| - | [[Category: Protein biosynthesis]]
| + | [[Category: Soll D]] |
| - | [[Category: Pyridoxal phosphate]]
| + | |
| - | [[Category: Pyridoxal-5'-phosphate]]
| + | |
| - | [[Category: Selenium]]
| + | |
| - | [[Category: Selenocysteine biosynthesis]]
| + | |
| - | [[Category: Seven-stranded bete-strand]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
SPCS_METMP Converts O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The micronutrient selenium is present in proteins as selenocysteine (Sec). In eukaryotes and archaea, Sec is formed in a tRNA-dependent conversion of O-phosphoserine (Sep) by O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS). Here, we present the crystal structure of Methanococcus maripaludis SepSecS complexed with PLP at 2.5 A resolution. SepSecS, a member of the Fold Type I PLP enzyme family, forms an (alpha2)2 homotetramer through its N-terminal extension. The active site lies on the dimer interface with each monomer contributing essential residues. In contrast to other Fold Type I PLP enzymes, Asn247 in SepSecS replaces the conserved Asp in binding the pyridinium nitrogen of PLP. A structural comparison with Escherichia coli selenocysteine lyase allowed construction of a model of Sep binding to the SepSecS catalytic site. Mutations of three conserved active site arginines (Arg72, Arg94, Arg307), protruding from the neighboring subunit, led to loss of in vivo and in vitro activity. The lack of active site cysteines demonstrates that a perselenide is not involved in SepSecS-catalyzed Sec formation; instead, the conserved arginines may facilitate the selenation reaction. Structural phylogeny shows that SepSecS evolved early in the history of PLP enzymes, and indicates that tRNA-dependent Sec formation is a primordial process.
Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation.,Araiso Y, Palioura S, Ishitani R, Sherrer RL, O'Donoghue P, Yuan J, Oshikane H, Domae N, Defranco J, Soll D, Nureki O Nucleic Acids Res. 2008 Mar;36(4):1187-99. Epub 2007 Dec 23. PMID:18158303[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Yuan J, Palioura S, Salazar JC, Su D, O'Donoghue P, Hohn MJ, Cardoso AM, Whitman WB, Soll D. RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proc Natl Acad Sci U S A. 2006 Dec 12;103(50):18923-7. Epub 2006 Dec 1. PMID:17142313 doi:http://dx.doi.org/10.1073/pnas.0609703104
- ↑ Araiso Y, Palioura S, Ishitani R, Sherrer RL, O'Donoghue P, Yuan J, Oshikane H, Domae N, Defranco J, Soll D, Nureki O. Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation. Nucleic Acids Res. 2008 Mar;36(4):1187-99. Epub 2007 Dec 23. PMID:18158303 doi:10.1093/nar/gkm1122
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