4RB4

Crystal structure of dodecameric iron-containing heptosyltransferase TibC in complex with ADP-D-beta-D-heptose at 3.9 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.88 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.283 

wwPDB Validation 3D Report Full Report



Literature

A structural mechanism for bacterial autotransporter glycosylation by a dodecameric heptosyltransferase family

Yao, Q.Lu, Q.Wan, X.Song, F.Xu, Y.Hu, M.Zamyatina, A.Liu, X.Huang, N.Zhu, P.Shao, F.

(2014) Elife 3

  • DOI: 10.7554/eLife.03714
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A large group of bacterial virulence autotransporters including AIDA-I from diffusely adhering E. coli (DAEC) and TibA from enterotoxigenic E. coli (ETEC) require hyperglycosylation for functioning. Here we demonstrate that TibC from ETEC harbors a h ...

    A large group of bacterial virulence autotransporters including AIDA-I from diffusely adhering E. coli (DAEC) and TibA from enterotoxigenic E. coli (ETEC) require hyperglycosylation for functioning. Here we demonstrate that TibC from ETEC harbors a heptosyltransferase activity on TibA and AIDA-I, defining a large family of bacterial autotransporter heptosyltransferases (BAHTs). The crystal structure of TibC reveals a characteristic ring-shape dodecamer. The protomer features an N-terminal β-barrel, a catalytic domain, a β-hairpin thumb, and a unique iron-finger motif. The iron-finger motif contributes to back-to-back dimerization; six dimers form the ring through β-hairpin thumb-mediated hand-in-hand contact. The structure of ADP-D-glycero-β-D-manno-heptose (ADP-D,D-heptose)-bound TibC reveals a sugar transfer mechanism and also the ligand stereoselectivity determinant. Electron-cryomicroscopy analyses uncover a TibC-TibA dodecamer/hexamer assembly with two enzyme molecules binding to one TibA substrate. The complex structure also highlights a high efficient hyperglycosylation of six autotransporter substrates simultaneously by the dodecamer enzyme complex.


    Organizational Affiliation

    Dr Feng Shao's Laboratory, National Institute of Biological Sciences, Beijing, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycosyltransferase tibC
A, B, C, D, E, F, G, H, I, J, K, L
406Escherichia coli DEC13EMutation(s): 1 
Gene Names: tibCECDEC13E_2355
EC: 2.4
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AQH
Query on AQH

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate
C17 H27 N5 O16 P2
KMSFWBYFWSKGGR-GZNZTODLSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
C, I, J
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.88 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.283 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.292α = 90
b = 313.196β = 101.26
c = 164.695γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-09-12 
  • Released Date: 2014-11-05 
  • Deposition Author(s): Yao, Q., Lu, Q., Shao, F.

Revision History 

  • Version 1.0: 2014-11-05
    Type: Initial release