5wxk: Difference between revisions

Line 1:

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

~~The entry~~ 5wxk is ~~ON HOLD until Paper~~ Publication

==EarP bound with domain I of EF-P==

== Structural highlights ==

<table><tr><td colspan='2'>[[5wxk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WXK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WXK 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=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>

<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5wxj|5wxj]], [[5wxi|5wxi]]</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=5wxk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wxk OCA], [http://pdbe.org/5wxk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wxk RCSB], [http://www.ebi.ac.uk/pdbsum/5wxk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wxk ProSAT]</span></td></tr>

</table>

== Function ==

[[http://www.uniprot.org/uniprot/E6MVW0_NEIMH E6MVW0_NEIMH]] Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase.[HAMAP-Rule:MF_00141]

== 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: Sengoku, T]]

[[Category: Yanagisawa, T]]

[[Category: Yokoyama, S]]

[[Category: Dtdp-rhamnose]]

[[Category: Ef-p]]

[[Category: Glycosyltransferase]]

[[Category: Gt-b]]

[[Category: Rhamnosylation]]

[[Category: Transferase]]

[[Category: Translation elongation]]

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5wxk is ON HOLD  until Paper Publication
+==EarP bound with domain I of EF-P==
+<StructureSection load='5wxk' size='340' side='right' caption='[[5wxk]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5wxk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WXK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WXK 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=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5wxj|5wxj]], [[5wxi|5wxi]]</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=5wxk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wxk OCA], [http://pdbe.org/5wxk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wxk RCSB], [http://www.ebi.ac.uk/pdbsum/5wxk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wxk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/E6MVW0_NEIMH E6MVW0_NEIMH]] Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase.[HAMAP-Rule:MF_00141]
+<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 5wxk" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Sengoku, T]]
+[[Category: Yanagisawa, T]]
+[[Category: Yokoyama, S]]
+[[Category: Dtdp-rhamnose]]
+[[Category: Ef-p]]
+[[Category: Glycosyltransferase]]
+[[Category: Gt-b]]
+[[Category: Rhamnosylation]]
+[[Category: Transferase]]
+[[Category: Translation elongation]]