6RTG | pdb_00006rtg

Crystal structure of the UDP-bound glycosyltransferase domain from the YGT toxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.223 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6RTG

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Inverse control of Rab proteins byYersiniaADP-ribosyltransferase and glycosyltransferase related to clostridial glucosylating toxins.

Ost, G.S.Wirth, C.Bogdanovic, X.Kao, W.C.Schorch, B.Aktories, P.J.K.Papatheodorou, P.Schwan, C.Schlosser, A.Jank, T.Hunte, C.Aktories, K.

(2020) Sci Adv 6: eaaz2094-eaaz2094

  • DOI: https://doi.org/10.1126/sciadv.aaz2094
  • Primary Citation Related Structures: 
    6RTG, 6RTH

  • PubMed Abstract: 

    We identified a glucosyltransferase (YGT) and an ADP-ribosyltransferase (YART) in Yersinia mollaretii , highly related to glucosylating toxins from Clostridium difficile , the cause of antibiotics-associated enterocolitis. Both Yersinia toxins consist of an amino-terminal enzyme domain, an autoprotease domain activated by inositol hexakisphosphate, and a carboxyl-terminal translocation domain. YGT N -acetylglucosaminylates Rab5 and Rab31 at Thr 52 and Thr 36 , respectively, thereby inactivating the Rab proteins. YART ADP-ribosylates Rab5 and Rab31 at Gln 79 and Gln 64 , respectively. This activates Rab proteins by inhibiting GTP hydrolysis. We determined the crystal structure of the glycosyltransferase domain of YGT (YGT G ) in the presence and absence of UDP at 1.9- and 3.4-Å resolution, respectively. Thereby, we identified a previously unknown potassium ion-binding site, which explains potassium ion-dependent enhanced glycosyltransferase activity in clostridial and related toxins. Our findings exhibit a novel type of inverse regulation of Rab proteins by toxins and provide new insights into the structure-function relationship of glycosyltransferase toxins.


  • Organizational Affiliation
    • Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 60.65 kDa 
  • Atom Count: 4,632 
  • Modeled Residue Count: 503 
  • Deposited Residue Count: 521 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RTX toxin and Ca2+-binding protein521Yersinia mollaretii ATCC 43969Mutation(s): 0 
Gene Names: ymoll0001_37990

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP

Query on UDP



Download:Ideal Coordinates CCD File
B [auth A]URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
C [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
D [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.223 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.27α = 90
b = 164.27β = 90
c = 47.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
autoSHARPphasing
PHENIXphasing
XSCALEdata scaling
XDSdata reduction
MxCuBEdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyCRC 746
German Federal Ministry for Education and ResearchGermanyEXC-2189

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Advisory, Data collection, Database references, Derived calculations