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 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.282 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 
    0.283 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


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: 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.


Macromolecules
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AQH
Query on AQH

Download Ideal Coordinates CCD File 
AA [auth B]
CA [auth F]
EA [auth G]
HA [auth I]
KA [auth J]
[(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
EDO
Query on EDO

Download Ideal Coordinates CCD File 
GA [auth I],
JA [auth J],
R [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
BA [auth F]
DA [auth G]
FA [auth I]
IA [auth J]
LA [auth A]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.88 Å
  • R-Value Free:  0.295 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.282 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 0.283 (Depositor) 
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



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AQHClick on this verticalbar to view details

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