2i4m: Difference between revisions

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-[[Image:2i4m.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2i4m", creates the "Structure Box" on the page.
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-{{STRUCTURE_2i4m|  PDB=2i4m  |  SCENE=  }}
-'''Rhodopseudomonas palustris prolyl-tRNA synthetase in complex with ProAMS'''
+==Rhodopseudomonas palustris prolyl-tRNA synthetase in complex with ProAMS==
+<StructureSection load='2i4m' size='340' side='right'caption='[[2i4m]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2i4m]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodopseudomonas_palustris Rhodopseudomonas palustris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I4M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I4M FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PSD:5-O-[N-(PROLYL)-SULFAMOYL]ADENOSINE'>PSD</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=2i4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i4m OCA], [https://pdbe.org/2i4m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i4m RCSB], [https://www.ebi.ac.uk/pdbsum/2i4m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i4m ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYP_RHOPA SYP_RHOPA] Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). Can inadvertently accommodate and process cysteine. The misacylated Cys-tRNA(Pro) is not edited by ProRS.[HAMAP-Rule:MF_01570]
+== 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/i4/2i4m_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=2i4m ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Prolyl-tRNA synthetases (ProRSs) are unique among synthetases in that they have diverse architectures, notably the variable presence of a cis-editing domain homologous to the freestanding deacylase proteins YbaK and ProX. Here, we describe crystal structures of two bacterial ProRSs from the pathogen Enterococcus faecalis, which possesses an editing domain, and from Rhodopseudomonas palustris, which does not. We compare the overall structure and binding mode of ATP and prolyl-adenylate with those of the archael/eukaryote-type ProRS from Thermus thermophilus. Although structurally more homologous to YbaK, which preferentially hydrolyzes Cys-tRNA(Pro), the editing domain of E. faecalis ProRS possesses key elements similar to ProX, with which it shares the activity of hydrolyzing Ala-tRNA(Pro). The structures give insight into the complex evolution of ProRSs, the mechanism of editing, and structural differences between prokaryotic- and eukaryotic-type ProRSs that can be exploited for antibiotic design.
-==Overview==
+Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain.,Crepin T, Yaremchuk A, Tukalo M, Cusack S Structure. 2006 Oct;14(10):1511-25. PMID:17027500<ref>PMID:17027500</ref>
-Prolyl-tRNA synthetases (ProRSs) are unique among synthetases in that they have diverse architectures, notably the variable presence of a cis-editing domain homologous to the freestanding deacylase proteins YbaK and ProX. Here, we describe crystal structures of two bacterial ProRSs from the pathogen Enterococcus faecalis, which possesses an editing domain, and from Rhodopseudomonas palustris, which does not. We compare the overall structure and binding mode of ATP and prolyl-adenylate with those of the archael/eukaryote-type ProRS from Thermus thermophilus. Although structurally more homologous to YbaK, which preferentially hydrolyzes Cys-tRNA(Pro), the editing domain of E. faecalis ProRS possesses key elements similar to ProX, with which it shares the activity of hydrolyzing Ala-tRNA(Pro). The structures give insight into the complex evolution of ProRSs, the mechanism of editing, and structural differences between prokaryotic- and eukaryotic-type ProRSs that can be exploited for antibiotic design.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-I4M is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhodopseudomonas_palustris Rhodopseudomonas palustris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I4M OCA].
+</div>
+<div class="pdbe-citations 2i4m" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain., Crepin T, Yaremchuk A, Tukalo M, Cusack S, Structure. 2006 Oct;14(10):1511-25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17027500 17027500]
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-[[Category: Proline--tRNA ligase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Rhodopseudomonas palustris]]
-[[Category: Single protein]]
+[[Category: Crepin T]]
-[[Category: Crepin, T.]]
+[[Category: Cusack S]]
-[[Category: Cusack, S.]]
+[[Category: Tukalo M]]
-[[Category: Tukalo, M.]]
+[[Category: Yaremchuk A]]
-[[Category: Yaremchuk, A.]]
-[[Category: Alpha beta]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 07:03:41 2008''