5WXI

EarP bound with dTDP-rhamnose (soaked)

Summary for 5WXI

• Entry DOI: 10.2210/pdb5wxi/pdb
• Related: 5WXJ 5WXK
• Descriptor: EarP, 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE, BETA-MERCAPTOETHANOL, ... (6 entities in total)
• Functional Keywords: glycosyltransferase, gt-b, ef-p, rhamnosylation, translation elongation, dtdp-rhamnose, transferase
• Biological source: Neisseria meningitidis serogroup B / serotype 15 (strain H44/76)
• Total number of polymer chains: 2
• Total formula weight: 90769.98

Authors

Sengoku, T.,Yokoyama, S.,Yanagisawa, T. (deposition date: 2017-01-07, release date: 2018-02-28, Last modification date: 2024-04-03)

Primary citation

Sengoku, T.,Suzuki, T.,Dohmae, N.,Watanabe, C.,Honma, T.,Hikida, Y.,Yamaguchi, Y.,Takahashi, H.,Yokoyama, S.,Yanagisawa, T.
Structural basis of protein arginine rhamnosylation by glycosyltransferase EarP
Nat. Chem. Biol., 14:368-374, 2018

PubMed Abstract: 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-β-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 β-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-β-L-rhamnose-binding loop of EarP. Rhamnosylation by EarP should occur via an S2 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.

PubMed: 29440735
DOI: 10.1038/s41589-018-0002-y

Experimental method

X-RAY DIFFRACTION (2 Å)