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==EarP bound with dTDP-rhamnose (soaked)==
==EarP bound with dTDP-rhamnose (soaked)==
<StructureSection load='5wxi' size='340' side='right' caption='[[5wxi]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='5wxi' size='340' side='right'caption='[[5wxi]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5wxi]] 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=5WXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WXI FirstGlance]. <br>
<table><tr><td colspan='2'>[[5wxi]] 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=5WXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WXI FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRH:2-DEOXY-THYMIDINE-BETA-L-RHAMNOSE'>TRH</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&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5wxj|5wxj]], [[5wxk|5wxk]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRH:2-DEOXY-THYMIDINE-BETA-L-RHAMNOSE'>TRH</scene></td></tr>
<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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5wxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wxi OCA], [https://pdbe.org/5wxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wxi RCSB], [https://www.ebi.ac.uk/pdbsum/5wxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wxi 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=5wxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wxi OCA], [http://pdbe.org/5wxi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wxi RCSB], [http://www.ebi.ac.uk/pdbsum/5wxi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wxi ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[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>  
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.
 
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5wxi" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Neimh]]
[[Category: Large Structures]]
[[Category: Sengoku, T]]
[[Category: Neisseria meningitidis H44/76]]
[[Category: Yanagisawa, T]]
[[Category: Sengoku T]]
[[Category: Yokoyama, S]]
[[Category: Yanagisawa T]]
[[Category: Dtdp-rhamnose]]
[[Category: Yokoyama S]]
[[Category: Ef-p]]
[[Category: Glycosyltransferase]]
[[Category: Gt-b]]
[[Category: Rhamnosylation]]
[[Category: Transferase]]
[[Category: Translation elongation]]

Latest revision as of 07:04, 3 April 2024

EarP bound with dTDP-rhamnose (soaked)

5wxi, resolution 2.00Å

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