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5xvr

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Current revision (10:20, 27 March 2024) (edit) (undo)
 
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==EarP bound with dTDP-rhamnose (co-crystal)==
==EarP bound with dTDP-rhamnose (co-crystal)==
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<StructureSection load='5xvr' size='340' side='right' caption='[[5xvr]], [[Resolution|resolution]] 1.63&Aring;' scene=''>
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<StructureSection load='5xvr' size='340' side='right'caption='[[5xvr]], [[Resolution|resolution]] 1.63&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5xvr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Neimh Neimh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XVR FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5xvr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_meningitidis_H44/76 Neisseria meningitidis H44/76]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XVR FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRH:2-DEOXY-THYMIDINE-BETA-L-RHAMNOSE'>TRH</scene></td></tr>
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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]] 1.63&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5wxi|5wxi]], [[5wxk|5wxk]], [[5wxj|5wxj]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRH:2-DEOXY-THYMIDINE-BETA-L-RHAMNOSE'>TRH</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NMH_0797 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=909420 NEIMH])</td></tr>
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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=5xvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvr OCA], [https://pdbe.org/5xvr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xvr RCSB], [https://www.ebi.ac.uk/pdbsum/5xvr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvr ProSAT]</span></td></tr>
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<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=5xvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvr OCA], [http://pdbe.org/5xvr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xvr RCSB], [http://www.ebi.ac.uk/pdbsum/5xvr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvr ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/EARP_NEIMH EARP_NEIMH] Protein-arginine rhamnosyltransferase that catalyzes the transfer of a single rhamnose to elongation factor P (EF-P) on 'Lys-32', a modification required for EF-P-dependent rescue of polyproline stalled ribosomes.<ref>PMID:29440735</ref>
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Protein glycosylation regulates many cellular processes. Numerous glycosyltransferases with broad substrate specificities have been structurally characterized. A novel inverting glycosyltransferase, EarP, specifically transfers rhamnose from dTDP-beta-L-rhamnose to Arg32 of bacterial translation elongation factor P (EF-P) to activate its function. Here we report a crystallographic study of Neisseria meningitidis EarP. The EarP structure contains two tandem Rossmann-fold domains, which classifies EarP in glycosyltransferase superfamily B. In contrast to other structurally characterized protein glycosyltransferases, EarP binds the entire beta-sheet structure of EF-P domain I through numerous interactions that specifically recognize its conserved residues. Thus Arg32 is properly located at the active site, and causes structural change in a conserved dTDP-beta-L-rhamnose-binding loop of EarP. Rhamnosylation by EarP should occur via an SN2 reaction, with Asp20 as the general base. The Arg32 binding and accompanying structural change of EarP may induce a change in the rhamnose-ring conformation suitable for the reaction.
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Structural basis of protein arginine rhamnosylation by glycosyltransferase EarP.,Sengoku T, Suzuki T, Dohmae N, Watanabe C, Honma T, Hikida Y, Yamaguchi Y, Takahashi H, Yokoyama S, Yanagisawa T Nat Chem Biol. 2018 Feb 13. pii: 10.1038/s41589-018-0002-y. doi:, 10.1038/s41589-018-0002-y. PMID:29440735<ref>PMID:29440735</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 5xvr" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Neimh]]
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[[Category: Large Structures]]
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[[Category: Sengoku, T]]
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[[Category: Neisseria meningitidis H44/76]]
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[[Category: Yanagisawa, T]]
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[[Category: Sengoku T]]
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[[Category: Yokoyama, S]]
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[[Category: Yanagisawa T]]
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[[Category: Dtdp-rhamnose]]
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[[Category: Yokoyama S]]
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[[Category: Ef-p]]
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[[Category: Glycosyltransferase]]
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[[Category: Gt-b]]
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[[Category: Rhamnosylation]]
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[[Category: Transferase]]
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[[Category: Translation elongation]]
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Current revision

EarP bound with dTDP-rhamnose (co-crystal)

PDB ID 5xvr

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