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- PDB-4rap: Crystal structure of bacterial iron-containing dodecameric glycos... -

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Basic information

Entry
Database: PDB / ID: 4rap
TitleCrystal structure of bacterial iron-containing dodecameric glycosyltransferase TibC from enterotoxigenic E.coli H10407
ComponentsGlycosyltransferase TibC
KeywordsTRANSFERASE / GT-B fold / TibA / ADP-heptose
Function / homology
Function and homology information


Transferases; Glycosyltransferases; Transferring other glycosyl groups / glycosyltransferase activity / metal ion binding
Similarity search - Function
Glycosyltransferase Aah/TibC / : / Glycosyltransferase TibC, N-terminal domain / Glycosyl transferase, family 9 / Glycosyltransferase family 9 (heptosyltransferase)
Similarity search - Domain/homology
: / Autotransporter heptosyltransferase TibC
Similarity search - Component
Biological speciesEscherichia coli ETEC H10407 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.881 Å
AuthorsYao, Q. / Lu, Q. / Xu, Y. / 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.
#1: Journal: Cell Host Microbe / Year: 2014
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
DepositionSep 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase TibC
B: Glycosyltransferase TibC
C: Glycosyltransferase TibC
D: Glycosyltransferase TibC
E: Glycosyltransferase TibC
F: Glycosyltransferase TibC
G: Glycosyltransferase TibC
H: Glycosyltransferase TibC
I: Glycosyltransferase TibC
J: Glycosyltransferase TibC
K: Glycosyltransferase TibC
L: Glycosyltransferase TibC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)555,04229
Polymers554,06212
Non-polymers98017
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28970 Å2
ΔGint-269 kcal/mol
Surface area185680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.794, 314.368, 164.527
Angle α, β, γ (deg.)90.00, 101.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycosyltransferase TibC


Mass: 46171.832 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli ETEC H10407 (bacteria)
Strain: H10407 / ETEC / Gene: tibC, ETEC_2140 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9S4K6, Transferases; Glycosyltransferases
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.02 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.881→20 Å / Num. obs: 194303 / % possible obs: 99.9 % / Observed criterion σ(F): 1.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHELXSphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.881→19.92 Å / SU ML: 0.42 / σ(F): 1.35 / Phase error: 26.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 9779 5.04 %RANDOM
Rwork0.2084 ---
all0.265 194303 --
obs0.2102 194199 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.881→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37096 0 32 3 37131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01338353
X-RAY DIFFRACTIONf_angle_d1.39552285
X-RAY DIFFRACTIONf_dihedral_angle_d15.20913717
X-RAY DIFFRACTIONf_chiral_restr0.1175533
X-RAY DIFFRACTIONf_plane_restr0.0086774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8808-2.91340.36012430.31435067X-RAY DIFFRACTION81
2.9134-2.94760.3563240.29716112X-RAY DIFFRACTION100
2.9476-2.98340.33763330.28846156X-RAY DIFFRACTION100
2.9834-3.02110.3363280.28046225X-RAY DIFFRACTION100
3.0211-3.06070.34943130.27836175X-RAY DIFFRACTION100
3.0607-3.10240.38723260.28726210X-RAY DIFFRACTION100
3.1024-3.14660.32332920.27066211X-RAY DIFFRACTION100
3.1466-3.19340.30683250.2646151X-RAY DIFFRACTION100
3.1934-3.24310.30833630.24766187X-RAY DIFFRACTION100
3.2431-3.2960.29933410.25476119X-RAY DIFFRACTION100
3.296-3.35260.32123240.26186229X-RAY DIFFRACTION100
3.3526-3.41330.31183550.24716145X-RAY DIFFRACTION100
3.4133-3.47860.27253210.22596195X-RAY DIFFRACTION100
3.4786-3.54920.25263090.21556209X-RAY DIFFRACTION100
3.5492-3.62590.27123220.21686175X-RAY DIFFRACTION100
3.6259-3.70970.26913400.20866197X-RAY DIFFRACTION100
3.7097-3.80190.25073360.19986226X-RAY DIFFRACTION100
3.8019-3.90390.25433510.20526092X-RAY DIFFRACTION100
3.9039-4.01790.23763140.19466248X-RAY DIFFRACTION100
4.0179-4.14650.20473470.18846156X-RAY DIFFRACTION100
4.1465-4.29320.21983470.17516147X-RAY DIFFRACTION100
4.2932-4.46330.19193420.1636199X-RAY DIFFRACTION100
4.4633-4.66390.17323380.1596189X-RAY DIFFRACTION100
4.6639-4.90640.19453110.15866225X-RAY DIFFRACTION100
4.9064-5.20860.18353360.16646166X-RAY DIFFRACTION100
5.2086-5.60250.20783290.18426192X-RAY DIFFRACTION100
5.6025-6.15120.25713150.19896240X-RAY DIFFRACTION100
6.1512-7.00710.24963230.21486189X-RAY DIFFRACTION100
7.0071-8.70390.20613400.19816239X-RAY DIFFRACTION100
8.7039-19.92070.2312910.21896149X-RAY DIFFRACTION98

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