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

Experimental Data Snapshot

  • Resolution: 3.88 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.283 

Starting Model: experimental
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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: https://doi.org/10.7554/eLife.03714
  • Primary Citation of Related Structures:  
    4RAP, 4RB4

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosyltransferase tibC406Escherichia coli DEC13EMutation(s): 1 
Gene Names: tibCECDEC13E_2355
EC: 2.4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AQH

Download Ideal Coordinates CCD File 
AA [auth B]
CA [auth F]
EA [auth G]
HA [auth I]
KA [auth J]
AA [auth B],
CA [auth F],
EA [auth G],
HA [auth I],
KA [auth J],
MA [auth A],
N [auth K],
P [auth L],
S [auth C],
U [auth D],
W [auth E],
Y [auth H]
[(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
Query on EDO

Download Ideal Coordinates CCD File 
GA [auth I],
JA [auth J],
R [auth C]
C2 H6 O2
Query on FE

Download Ideal Coordinates CCD File 
BA [auth F]
DA [auth G]
FA [auth I]
IA [auth J]
LA [auth A]
BA [auth F],
DA [auth G],
FA [auth I],
IA [auth J],
LA [auth A],
M [auth K],
O [auth L],
Q [auth C],
T [auth D],
V [auth E],
X [auth H],
Z [auth B]
Experimental Data & Validation

Experimental Data

  • 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
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description