2du3: Difference between revisions

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<StructureSection load='2du3' size='340' side='right'caption='[[2du3]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
<StructureSection load='2du3' size='340' side='right'caption='[[2du3]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2du3]] is a 3 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=2DU3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DU3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2du3]] is a 3 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=2DU3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DU3 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</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]] 2.6&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2du4|2du4]], [[2du5|2du5]], [[2du6|2du6]], [[2du7|2du7]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></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=2du3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2du3 OCA], [https://pdbe.org/2du3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2du3 RCSB], [https://www.ebi.ac.uk/pdbsum/2du3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2du3 ProSAT]</span></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=2du3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2du3 OCA], [https://pdbe.org/2du3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2du3 RCSB], [https://www.ebi.ac.uk/pdbsum/2du3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2du3 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/SEPS_ARCFU SEPS_ARCFU]] Catalyzes the attachment of O-phosphoserine (Sep) to tRNA(Cys) (Probable).[HAMAP-Rule:MF_01674]  
[https://www.uniprot.org/uniprot/SEPS_ARCFU SEPS_ARCFU] Catalyzes the attachment of O-phosphoserine (Sep) to tRNA(Cys) (Probable).[HAMAP-Rule:MF_01674]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=2du3 ConSurf].
</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=2du3 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Cysteine is ligated to tRNA(Cys) by cysteinyl-tRNA synthetase in most organisms. However, in methanogenic archaea lacking cysteinyl-tRNA synthetase, O-phosphoserine is ligated to tRNA(Cys) by O-phosphoseryl-tRNA synthetase (SepRS), and the phosphoseryl-tRNA(Cys) is converted to cysteinyl-tRNA(Cys). In this study, we determined the crystal structure of the SepRS tetramer in complex with tRNA(Cys) and O-phosphoserine at 2.6-A resolution. The catalytic domain of SepRS recognizes the negatively charged side chain of O-phosphoserine at a noncanonical site, using the dipole moment of a conserved alpha-helix. The unique C-terminal domain specifically recognizes the anticodon GCA of tRNA(Cys). On the basis of the structure, we engineered SepRS to recognize tRNA(Cys) mutants with the anticodons UCA and CUA and clarified the anticodon recognition mechanism by crystallography. The mutant SepRS-tRNA pairs may be useful for translational incorporation of O-phosphoserine into proteins in response to the stop codons UGA and UAG.
Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea.,Fukunaga R, Yokoyama S Nat Struct Mol Biol. 2007 Apr;14(4):272-9. Epub 2007 Mar 11. PMID:17351629<ref>PMID:17351629</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2du3" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Arcfl]]
[[Category: Archaeoglobus fulgidus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Fukunaga, R]]
[[Category: Fukunaga R]]
[[Category: Alpha4 tetramer]]
[[Category: Ligase-rna complex]]

Latest revision as of 13:48, 13 March 2024

Crystal structure of Archaeoglobus fulgidus O-phosphoseryl-tRNA synthetase complexed with tRNACys and O-phosphoserine

2du3, resolution 2.60Å

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