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- PDB-7u2p: Structure of TcdA GTD in complex with RhoA -

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Basic information

Entry
Database: PDB / ID: 7u2p
TitleStructure of TcdA GTD in complex with RhoA
Components
  • Glucosyltransferase TcdA
  • Transforming protein RhoA
KeywordsTOXIN / GTD
Function / homology
Function and homology information


RHO GTPases Activate ROCKs / SLIT2:ROBO1 increases RHOA activity / Sema4D mediated inhibition of cell attachment and migration / Sema4D induced cell migration and growth-cone collapse / RHO GTPases Activate Rhotekin and Rhophilins / RHO GTPases activate PKNs / Axonal growth stimulation / PCP/CE pathway / RHO GTPases activate KTN1 / Axonal growth inhibition (RHOA activation) ...RHO GTPases Activate ROCKs / SLIT2:ROBO1 increases RHOA activity / Sema4D mediated inhibition of cell attachment and migration / Sema4D induced cell migration and growth-cone collapse / RHO GTPases Activate Rhotekin and Rhophilins / RHO GTPases activate PKNs / Axonal growth stimulation / PCP/CE pathway / RHO GTPases activate KTN1 / Axonal growth inhibition (RHOA activation) / PI3K/AKT activation / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / EPHA-mediated growth cone collapse / ERBB2 Regulates Cell Motility / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / G beta:gamma signalling through PI3Kgamma / RHOC GTPase cycle / negative regulation of synapse assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RHO GTPases activate CIT / Ovarian tumor domain proteases / RHOA GTPase cycle / G alpha (12/13) signalling events / regulation of dendrite development / RHO GTPases Activate Formins / alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / regulation of modification of synaptic structure / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / regulation of osteoblast proliferation / negative regulation of vascular associated smooth muscle cell migration / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / regulation of neural precursor cell proliferation / cleavage furrow formation / regulation of modification of postsynaptic actin cytoskeleton / positive regulation of smooth muscle contraction / forebrain radial glial cell differentiation / apical junction assembly / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / regulation of systemic arterial blood pressure by endothelin / beta selection / establishment of epithelial cell apical/basal polarity / negative regulation of cell size / VEGFA-VEGFR2 Pathway / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / stress-activated protein kinase signaling cascade / odontogenesis / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / GTP metabolic process / negative regulation of cell-substrate adhesion / positive regulation of alpha-beta T cell differentiation / positive regulation of leukocyte adhesion to vascular endothelial cell / motor neuron apoptotic process / wound healing, spreading of cells / microtubule depolymerization / apical junction complex / ossification involved in bone maturation / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / positive regulation of actin filament polymerization / negative chemotaxis / Rho GDP-dissociation inhibitor binding / myosin binding / stress fiber assembly / positive regulation of cytokinesis / regulation of neuron projection development / androgen receptor signaling pathway / cerebral cortex cell migration / glycosyltransferase activity / negative regulation of vascular associated smooth muscle cell proliferation / cleavage furrow / regulation of calcium ion transport / Rho protein signal transduction / semaphorin-plexin signaling pathway / negative regulation of neuron differentiation / mitotic spindle assembly / endothelial cell migration / positive regulation of T cell migration / regulation of microtubule cytoskeleton organization / negative regulation of canonical NF-kappaB signal transduction / cytoplasmic microtubule organization / negative regulation of reactive oxygen species biosynthetic process / skeletal muscle tissue development / cysteine-type peptidase activity / positive regulation of stress fiber assembly / cytoskeleton organization / positive regulation of neuron differentiation / regulation of cell migration / Neutrophil degranulation / cell-matrix adhesion
Similarity search - Function
TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. ...TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Small GTPase Rho / small GTPase Rho family profile. / Nucleotide-diphospho-sugar transferases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Toxin A / Transforming protein RhoA
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.596 Å
AuthorsBaohua, C. / Zheng, L. / Kay, P. / Rongsheng, J.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI125704 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI139087 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI158503 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI156092 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124165 United States
CitationJournal: Sci Rep / Year: 2022
Title: Structure of the glucosyltransferase domain of TcdA in complex with RhoA provides insights into substrate recognition.
Authors: Chen, B. / Liu, Z. / Perry, K. / Jin, R.
History
DepositionFeb 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucosyltransferase TcdA
B: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9967
Polymers83,8112
Non-polymers1,1855
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-66 kcal/mol
Surface area32260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.641, 122.798, 127.474
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Glucosyltransferase TcdA


Mass: 62918.996 Da / Num. of mol.: 1 / Mutation: K190A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdA, toxA / Production host: Escherichia coli (E. coli)
References: UniProt: P16154, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Protein Transforming protein RhoA


Mass: 20891.910 Da / Num. of mol.: 1 / Mutation: T37N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Rhoa, Arha, Arha2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QUI0, small monomeric GTPase

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Non-polymers , 6 types, 57 molecules

#3: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M MES, pH 5.9, and 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.596→83.799 Å / Num. obs: 27633 / % possible obs: 98.5 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.79
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.902 / Num. unique obs: 2667 / CC1/2: 0.587

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIXphasing
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTN, 3SRZ

1ftn

3srz


Resolution: 2.596→83.799 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.942 / SU B: 14.399 / SU ML: 0.278 / Cross valid method: FREE R-VALUE / ESU R: 0.857 / ESU R Free: 0.296
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2354 1276 4.618 %
Rwork0.2149 26357 -
all0.216 --
obs-27633 98.146 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 60.029 Å2
Baniso -1Baniso -2Baniso -3
1-4.628 Å20 Å20 Å2
2---3.849 Å20 Å2
3----0.779 Å2
Refinement stepCycle: LAST / Resolution: 2.596→83.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5810 0 71 52 5933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125989
X-RAY DIFFRACTIONr_angle_refined_deg1.1091.6518108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1125719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23623.956316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.466151097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1971528
X-RAY DIFFRACTIONr_chiral_restr0.0890.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024479
X-RAY DIFFRACTIONr_nbd_refined0.2150.22758
X-RAY DIFFRACTIONr_nbtor_refined0.3180.24199
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.2191
X-RAY DIFFRACTIONr_metal_ion_refined0.0860.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3470.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2880.25
X-RAY DIFFRACTIONr_mcbond_it3.1565.9542882
X-RAY DIFFRACTIONr_mcangle_it4.8498.933599
X-RAY DIFFRACTIONr_scbond_it3.8136.0763107
X-RAY DIFFRACTIONr_scangle_it5.5149.0334509
X-RAY DIFFRACTIONr_lrange_it7.56279.6259114
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.596-2.6630.367830.33317960.33420420.5730.62692.01760.318
2.663-2.7360.357960.32618640.32720070.6610.70697.65820.298
2.736-2.8150.3241110.31418350.31419490.7630.75799.84610.291
2.815-2.9020.2691120.29817780.29618930.8160.79699.84150.268
2.902-2.9970.354740.27817730.28118500.7890.8399.83780.25
2.997-3.1020.285850.26116830.26217760.8650.85399.54960.229
3.102-3.2190.369700.25416360.25817110.8260.87199.70780.224
3.219-3.350.334650.24515920.24916620.8620.89199.69920.214
3.35-3.4990.206690.22515090.22515930.9290.92199.05840.205
3.499-3.6690.245940.20914110.21115200.930.94299.01320.189
3.669-3.8670.183630.19513440.19414460.9590.95397.30290.181
3.867-4.1010.195600.18612760.18713840.9510.95696.53180.172
4.101-4.3840.184570.17812360.17813030.9620.96399.23250.167
4.384-4.7340.178350.15311480.15411980.9590.96798.74790.143
4.734-5.1840.216480.16910590.1711230.9490.96398.57520.159
5.184-5.7930.204390.1989640.19810230.9610.95598.0450.186
5.793-6.6840.282430.2488430.259040.9330.9498.00890.226
6.684-8.1730.207350.1956930.1957810.9560.95693.21380.19
8.173-11.5040.11250.1485720.1466160.9830.97796.91560.165
11.504-83.7990.208120.2423450.2413740.9720.95695.45450.259

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