5wxj: Difference between revisions

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~~'''Unreleased structure'''~~

The ~~entry 5wxj~~ is ~~ON HOLD~~

==Apo EarP==

== Structural highlights ==

<table><tr><td colspan='2'>[[5wxj]] 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=5WXJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WXJ 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]] 1.85Å</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></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=5wxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wxj OCA], [https://pdbe.org/5wxj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wxj RCSB], [https://www.ebi.ac.uk/pdbsum/5wxj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wxj ProSAT]</span></td></tr>

</table>

== Function ==

[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>

== Publication Abstract from PubMed ==

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.

~~Authors~~:

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>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Neisseria meningitidis H44/76]]

[[Category: Sengoku T]]

[[Category: Yanagisawa T]]

[[Category: Yokoyama S]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5wxj is ON HOLD
+==Apo EarP==
+<StructureSection load='5wxj' size='340' side='right'caption='[[5wxj]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5wxj]] 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=5WXJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WXJ 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]] 1.85&#8491;</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></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=5wxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wxj OCA], [https://pdbe.org/5wxj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wxj RCSB], [https://www.ebi.ac.uk/pdbsum/5wxj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wxj ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-Authors:
+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>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5wxj" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Neisseria meningitidis H44/76]]
+[[Category: Sengoku T]]
+[[Category: Yanagisawa T]]
+[[Category: Yokoyama S]]