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- PDB-4rb4: Crystal structure of dodecameric iron-containing heptosyltransfer... -

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Basic information

Entry
Database: PDB / ID: 4rb4
TitleCrystal structure of dodecameric iron-containing heptosyltransferase TibC in complex with ADP-D-beta-D-heptose at 3.9 angstrom resolution
ComponentsGlycosyltransferase tibC
KeywordsTRANSFERASE / GT-B fold / Heptose transfer / TibA / ADP-D-beta-D-heptose
Function / homologyChem-AQH / : / :
Function and homology information
Biological speciesEscherichia coli DEC13E (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.88 Å
AuthorsYao, Q. / Lu, Q. / Shao, F.
CitationJournal: 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
DepositionSep 12, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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.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_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
K: Glycosyltransferase tibC
L: Glycosyltransferase tibC
C: Glycosyltransferase tibC
D: Glycosyltransferase tibC
E: Glycosyltransferase tibC
H: Glycosyltransferase tibC
B: Glycosyltransferase tibC
F: Glycosyltransferase tibC
G: Glycosyltransferase tibC
I: Glycosyltransferase tibC
J: Glycosyltransferase tibC
A: Glycosyltransferase tibC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)564,30339
Polymers556,01412
Non-polymers8,28927
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28010 Å2
ΔGint-226 kcal/mol
Surface area184250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.292, 313.196, 164.695
Angle α, β, γ (deg.)90.00, 101.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11K
21L
31C
41D
51E
61H
71B
81F
91G
101I
111J
121A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PHEPHEKA9 - 3759 - 375
2PHEPHELB9 - 3759 - 375
3ILEILECC10 - 37510 - 375
4ILEILEDD10 - 37510 - 375
5ILEILEEE10 - 37510 - 375
6ILEILEHF10 - 37510 - 375
7PHEPHEBG9 - 3759 - 375
8PHEPHEFH9 - 3759 - 375
9THRTHRGI11 - 37511 - 375
10ILEILEIJ10 - 37510 - 375
11PHEPHEJK9 - 3759 - 375
12ILEILEAL10 - 37510 - 375

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.979165, 0.112159, 0.169283), (0.140222, -0.229533, 0.963147), (0.146882, 0.966817, 0.209023)7.74355, 35.71316, -30.09583

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Components

#1: Protein
Glycosyltransferase tibC


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 / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-AQH / [(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


Mass: 619.368 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C17H27N5O16P2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2

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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: Jun 29, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 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

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4RAP

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
RfactorNum. reflection% reflectionSelection details
Rfree0.29457 3995 5 %RANDOM
Rwork0.28197 ---
all0.2826 76851 --
obs0.2826 75852 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 148.073 Å2
Baniso -1Baniso -2Baniso -3
1-10.59 Å20 Å23.42 Å2
2---8.69 Å20 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 3.88→20.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37107 0 504 0 37611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01938835
X-RAY DIFFRACTIONr_bond_other_d0.0070.0235610
X-RAY DIFFRACTIONr_angle_refined_deg0.2381.95153034
X-RAY DIFFRACTIONr_angle_other_deg0.397381751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2654605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31422.7741846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.192155837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.18315299
X-RAY DIFFRACTIONr_chiral_restr0.4220.25654
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02143787
X-RAY DIFFRACTIONr_gen_planes_other0.0070.029788
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5405 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1KMEDIUM POSITIONAL0.320.5
2LMEDIUM POSITIONAL0.520.5
3CMEDIUM POSITIONAL0.240.5
4DMEDIUM POSITIONAL0.50.5
5EMEDIUM POSITIONAL0.290.5
6HMEDIUM POSITIONAL0.390.5
7BMEDIUM POSITIONAL0.280.5
8FMEDIUM POSITIONAL0.290.5
9GMEDIUM POSITIONAL0.40.5
10IMEDIUM POSITIONAL0.30.5
11JMEDIUM POSITIONAL0.240.5
12AMEDIUM POSITIONAL0.330.5
1KMEDIUM THERMAL2.962
2LMEDIUM THERMAL12.692
3CMEDIUM THERMAL2.782
4DMEDIUM THERMAL4.062
5EMEDIUM THERMAL4.142
6HMEDIUM THERMAL3.222
7BMEDIUM THERMAL3.112
8FMEDIUM THERMAL4.022
9GMEDIUM THERMAL3.12
10IMEDIUM THERMAL6.072
11JMEDIUM THERMAL2.942
12AMEDIUM THERMAL3.472
LS refinement shellResolution: 3.879→3.979 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 280 -
Rwork0.361 5288 -
obs--93.64 %

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