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- PDB-4rap: Crystal structure of bacterial iron-containing dodecameric glycos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rap | ||||||
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Title | Crystal structure of bacterial iron-containing dodecameric glycosyltransferase TibC from enterotoxigenic E.coli H10407 | ||||||
![]() | Glycosyltransferase TibC | ||||||
![]() | TRANSFERASE / GT-B fold / TibA / ADP-heptose | ||||||
Function / homology | Glycosyltransferase Aah/TibC / Glycosyl transferase, family 9 / Glycosyltransferase family 9 (heptosyltransferase) / Transferases; Glycosyltransferases / glycosyltransferase activity / : / Glycosyltransferase TibC![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yao, Q. / Lu, Q. / Xu, Y. / Shao, F. | ||||||
![]() | ![]() Title: A structural mechanism for bacterial autotransporter glycosylation by a dodecameric heptosyltransferase family. Authors: Qing Yao / Qiuhe Lu / Xiaobo Wan / Feng Song / Yue Xu / Mo Hu / Alla Zamyatina / Xiaoyun Liu / Niu Huang / Ping Zhu / Feng Shao / ![]() ![]() 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. ...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. #1: ![]() Title: An iron-containing dodecameric heptosyltransferase family modifies bacterial autotransporters in pathogenesis. Authors: Lu, Q. / Yao, Q. / Xu, Y. / Li, L. / Li, S. / Liu, Y. / Gao, W. / Niu, M. / Sharon, M. / Ben-Nissan, G. / Zamyatina, A. / Liu, X. / Chen, S. / Shao, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 888.2 KB | Display | ![]() |
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PDB format | ![]() | 763.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 575.6 KB | Display | ![]() |
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Full document | ![]() | 726.2 KB | Display | |
Data in XML | ![]() | 168.7 KB | Display | |
Data in CIF | ![]() | 218.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46171.832 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: H10407 / ETEC / Gene: tibC, ETEC_2140 / Production host: ![]() ![]() References: UniProt: Q9S4K6, Transferases; Glycosyltransferases #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 8% PEG 8000, 120mM magnesium acetate, 100mM MES buffer pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.881→20 Å / Num. obs: 194303 / % possible obs: 99.9 % / Observed criterion σ(F): 1.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.881→19.92 Å
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Refine LS restraints |
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LS refinement shell |
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