2hl0

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[[Image:2hl0.gif|left|200px]]
 
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{{Structure
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==Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with seryl-3'-aminoadenosine==
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|PDB= 2hl0 |SIZE=350|CAPTION= <scene name='initialview01'>2hl0</scene>, resolution 1.86&Aring;
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<StructureSection load='2hl0' size='340' side='right'caption='[[2hl0]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=A3S:SERINE-3&#39;-AMINOADENOSINE'>A3S</scene>
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<table><tr><td colspan='2'>[[2hl0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HL0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HL0 FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Threonine--tRNA_ligase Threonine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.3 6.1.1.3] </span>
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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]] 1.86&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A3S:SERINE-3-AMINOADENOSINE'>A3S</scene></td></tr>
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|DOMAIN=
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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=2hl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hl0 OCA], [https://pdbe.org/2hl0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hl0 RCSB], [https://www.ebi.ac.uk/pdbsum/2hl0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hl0 ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1y2q|1Y2Q]], [[2hkz|2HKZ]], [[2hl1|2HL1]], [[2hl2|2HL2]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hl0 OCA], [http://www.ebi.ac.uk/pdbsum/2hl0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2hl0 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/SYT_PYRAB SYT_PYRAB]
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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/hl/2hl0_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=2hl0 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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To ensure a high fidelity during translation, threonyl-tRNA synthetases (ThrRSs) harbor an editing domain that removes noncognate L-serine attached to tRNAThr. Most archaeal ThrRSs possess a unique editing domain structurally similar to D-aminoacyl-tRNA deacylases (DTDs) found in eubacteria and eukaryotes that specifically removes D-amino acids attached to tRNA. Here, we provide mechanistic insights into the removal of noncognate L-serine from tRNAThr by a DTD-like editing module from Pyrococcus abyssi ThrRS (Pab-NTD). High-resolution crystal structures of Pab-NTD with pre- and post-transfer substrate analogs and with L-serine show mutually nonoverlapping binding sites for the seryl moiety. Although the pre-transfer editing is excluded, the analysis reveals the importance of main chain atoms in proper positioning of the post-transfer substrate for its hydrolysis. A single residue has been shown to play a pivotal role in the inversion of enantioselectivity both in Pab-NTD and DTD. The study identifies an enantioselectivity checkpoint that filters opposite chiral molecules and thus provides a fascinating example of how nature has subtly engineered this domain for the selection of chiral molecules during translation.
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'''Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with seryl-3'-aminoadenosine'''
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Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea.,Hussain T, Kruparani SP, Pal B, Dock-Bregeon AC, Dwivedi S, Shekar MR, Sureshbabu K, Sankaranarayanan R EMBO J. 2006 Sep 6;25(17):4152-62. Epub 2006 Aug 10. PMID:16902403<ref>PMID:16902403</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2hl0" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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To ensure a high fidelity during translation, threonyl-tRNA synthetases (ThrRSs) harbor an editing domain that removes noncognate L-serine attached to tRNAThr. Most archaeal ThrRSs possess a unique editing domain structurally similar to D-aminoacyl-tRNA deacylases (DTDs) found in eubacteria and eukaryotes that specifically removes D-amino acids attached to tRNA. Here, we provide mechanistic insights into the removal of noncognate L-serine from tRNAThr by a DTD-like editing module from Pyrococcus abyssi ThrRS (Pab-NTD). High-resolution crystal structures of Pab-NTD with pre- and post-transfer substrate analogs and with L-serine show mutually nonoverlapping binding sites for the seryl moiety. Although the pre-transfer editing is excluded, the analysis reveals the importance of main chain atoms in proper positioning of the post-transfer substrate for its hydrolysis. A single residue has been shown to play a pivotal role in the inversion of enantioselectivity both in Pab-NTD and DTD. The study identifies an enantioselectivity checkpoint that filters opposite chiral molecules and thus provides a fascinating example of how nature has subtly engineered this domain for the selection of chiral molecules during translation.
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*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2HL0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HL0 OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea., Hussain T, Kruparani SP, Pal B, Dock-Bregeon AC, Dwivedi S, Shekar MR, Sureshbabu K, Sankaranarayanan R, EMBO J. 2006 Sep 6;25(17):4152-62. Epub 2006 Aug 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16902403 16902403]
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[[Category: Pyrococcus abyssi]]
[[Category: Pyrococcus abyssi]]
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[[Category: Single protein]]
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[[Category: Hussain T]]
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[[Category: Threonine--tRNA ligase]]
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[[Category: Kruparani SP]]
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[[Category: Hussain, T.]]
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[[Category: Pal B]]
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[[Category: Kruparani, S P.]]
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[[Category: Sankaranarayanan R]]
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[[Category: Pal, B.]]
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[[Category: Sankaranarayanan, R.]]
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[[Category: aminoacyl-trna synthetase]]
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[[Category: editing]]
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[[Category: enantioselectivity]]
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[[Category: enzyme mechanism]]
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[[Category: translation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:31:48 2008''
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Current revision

Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with seryl-3'-aminoadenosine

PDB ID 2hl0

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