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| | <StructureSection load='2i4m' size='340' side='right'caption='[[2i4m]], [[Resolution|resolution]] 2.80Å' scene=''> | | <StructureSection load='2i4m' size='340' side='right'caption='[[2i4m]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2i4m]] is a 3 chain structure with sequence from [https://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=2I4M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I4M FirstGlance]. <br> | + | <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='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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">proS,RPA2928 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1076 "Rhodobacillus palustris" Molisch 1907])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Proline--tRNA_ligase Proline--tRNA ligase], with EC number [https://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=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> | | <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> | | </table> |
| | == Function == | | == 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]
| + | [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]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Rhodobacillus palustris molisch 1907]] | |
| | [[Category: Large Structures]] | | [[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]]
| + | |
| Structural highlights
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Crepin T, Yaremchuk A, Tukalo M, Cusack S. Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain. Structure. 2006 Oct;14(10):1511-25. PMID:17027500 doi:http://dx.doi.org/10.1016/j.str.2006.08.007
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