2i4l: Difference between revisions

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==Rhodopseudomonas palustris prolyl-tRNA synthetase==
==Rhodopseudomonas palustris prolyl-tRNA synthetase==
<StructureSection load='2i4l' size='340' side='right' caption='[[2i4l]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='2i4l' size='340' side='right'caption='[[2i4l]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2i4l]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"rhodobacillus_palustris"_molisch_1907 "rhodobacillus palustris" molisch 1907]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I4L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I4L FirstGlance]. <br>
<table><tr><td colspan='2'>[[2i4l]] 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=2I4L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I4L FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">proS,RPA2928 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1076 "Rhodobacillus palustris" Molisch 1907])</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&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proline--tRNA_ligase Proline--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.15 6.1.1.15] </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=2i4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i4l OCA], [https://pdbe.org/2i4l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i4l RCSB], [https://www.ebi.ac.uk/pdbsum/2i4l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i4l 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=2i4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i4l OCA], [http://pdbe.org/2i4l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2i4l RCSB], [http://www.ebi.ac.uk/pdbsum/2i4l PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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]  
[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 ==
== 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/i4/2i4l_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i4/2i4l_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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/chain_selection.php?pdb_ID=2ata 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=2i4l ConSurf].
<div style="clear:both"></div>
<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.
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>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2i4l" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]]
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Rhodobacillus palustris molisch 1907]]
[[Category: Large Structures]]
[[Category: Proline--tRNA ligase]]
[[Category: Rhodopseudomonas palustris]]
[[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]]
[[Category: Ligase]]

Latest revision as of 12:01, 21 February 2024

Rhodopseudomonas palustris prolyl-tRNA synthetaseRhodopseudomonas palustris prolyl-tRNA synthetase

Structural highlights

2i4l is a 3 chain structure with sequence from Rhodopseudomonas palustris. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2i4l, resolution 2.00Å

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