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Yorodumi- PDB-4rb4: Crystal structure of dodecameric iron-containing heptosyltransfer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rb4 | ||||||
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Title | Crystal structure of dodecameric iron-containing heptosyltransferase TibC in complex with ADP-D-beta-D-heptose at 3.9 angstrom resolution | ||||||
Components | Glycosyltransferase tibC | ||||||
Keywords | TRANSFERASE / GT-B fold / Heptose transfer / TibA / ADP-D-beta-D-heptose | ||||||
Function / homology | Chem-AQH / : / : Function and homology information | ||||||
Biological species | Escherichia coli DEC13E (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.88 Å | ||||||
Authors | Yao, Q. / Lu, Q. / Shao, F. | ||||||
Citation | Journal: Elife / Year: 2014 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rb4.cif.gz | 798.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rb4.ent.gz | 644.7 KB | Display | PDB format |
PDBx/mmJSON format | 4rb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rb4_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 4rb4_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 4rb4_validation.xml.gz | 166.3 KB | Display | |
Data in CIF | 4rb4_validation.cif.gz | 214 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/4rb4 ftp://data.pdbj.org/pub/pdb/validation_reports/rb/4rb4 | HTTPS FTP |
-Related structure data
Related structure data | 2755C 2756C 2757C 2758C 4rapSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4
NCS oper:
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-Components
#1: Protein | Mass: 46334.500 Da / Num. of mol.: 12 / Mutation: D110A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli DEC13E (bacteria) / Gene: tibC, ECDEC13E_2355 / Production host: Escherichia coli (E. coli) References: UniProt: H5MH13, Transferases; Glycosyltransferases #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-AQH / [( #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2014 |
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: 3.88→20.04 Å / Num. all: 76251 / Num. obs: 75852 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4RAP Resolution: 3.88→20.04 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.859 / SU B: 45.451 / SU ML: 0.613 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.822 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: B VALUES HAVE BEEN FIXED IN THE REFINEMENT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 148.073 Å2
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Refinement step | Cycle: LAST / Resolution: 3.88→20.04 Å
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Refine LS restraints |
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