5wxi

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:04, 3 April 2024) (edit) (undo)
 
Line 1: Line 1:
==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]]
+

Current revision

EarP bound with dTDP-rhamnose (soaked)

PDB ID 5wxi

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5wxi"
Personal tools