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- PDB-8ui6: X-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex... -

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Basic information

Entry
Database: PDB / ID: 8ui6
TitleX-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with UDP-GalNAc, Mn2+, and Muc5AC-3,13
Components
  • Glycosyl transferaseGlycosyltransferase
  • Mucin-5AC
KeywordsTRANSFERASE / GT-A fold GalNAc Glycosyltransferase / Mucin-type O-glycosylation / Toxoplasma gondii cyst wall glycosylation
Function / homology
Function and homology information


mucus layer / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / extracellular matrix structural constituent / Dectin-2 family ...mucus layer / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / extracellular matrix structural constituent / Dectin-2 family / extracellular matrix / Golgi lumen / carbohydrate binding / Golgi apparatus / extracellular space / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
WxxW domain / Mucin-2 protein WxxW repeating region / N-acetylgalactosaminyltransferase / Galactosyltransferase, C-terminal / N-terminal domain of galactosyltransferase / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain ...WxxW domain / Mucin-2 protein WxxW repeating region / N-acetylgalactosaminyltransferase / Galactosyltransferase, C-terminal / N-terminal domain of galactosyltransferase / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / C-terminal cystine knot signature. / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Glycosyltransferase 2-like / Glycosyl transferase family 2 / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Ricin-type beta-trefoil lectin domain / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / : / URIDINE-5'-DIPHOSPHATE / Glycosyl transferase / Mucin-5AC
Similarity search - Component
Biological speciesToxoplasma gondii ME49 (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKumar, P. / Samara, N.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)1-ZIA-DE000754-03 United States
CitationJournal: Nat Commun / Year: 2024
Title: A Toxoplasma gondii O-glycosyltransferase that modulates bradyzoite cyst wall rigidity is distinct from host homologues.
Authors: Kumar, P. / Tomita, T. / Gerken, T.A. / Ballard, C.J. / Lee, Y.S. / Weiss, L.M. / Samara, N.L.
History
DepositionOct 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl transferase
B: Mucin-5AC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9457
Polymers65,0162
Non-polymers9295
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.252, 66.913, 163.581
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AB

#1: Protein Glycosyl transferase / Glycosyltransferase


Mass: 63514.129 Da / Num. of mol.: 1 / Mutation: g297s
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii ME49 (eukaryote) / Gene: TGME49_318730 / Plasmid: pPICz-alpha
Details (production host): His Tag (6x), c-Myc Epitope Tag, TEV protease cleavage site
Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168
References: UniProt: A0A125YMZ8, polypeptide N-acetylgalactosaminyltransferase
#2: Protein/peptide Mucin-5AC / MUC-5AC / Gastric mucin / Major airway glycoprotein / Mucin-5 subtype AC / tracheobronchial / ...MUC-5AC / Gastric mucin / Major airway glycoprotein / Mucin-5 subtype AC / tracheobronchial / Tracheobronchial mucin / TBM


Mass: 1501.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P98088
#6: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 24 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.1 M CHES pH 9.5 and 14-20% PEG 8000 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 1, 2022
RadiationMonochromator: FMB OXFORD single crystal side bounce monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. obs: 20128 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 52.15 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.06 / Rrim(I) all: 0.161 / Net I/σ(I): 14.8
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.28 / Num. unique obs: 961 / CC1/2: 0.732 / CC star: 0.919 / Rpim(I) all: 0.37 / Rrim(I) all: 0.822 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SERGUIdata collection
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→19.98 Å / SU ML: 0.328 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.6168
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2315 2000 9.96 %
Rwork0.1745 18077 -
obs0.1801 20077 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.74 Å2
Refinement stepCycle: LAST / Resolution: 2.65→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4240 0 54 20 4314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274446
X-RAY DIFFRACTIONf_angle_d0.53016035
X-RAY DIFFRACTIONf_chiral_restr0.0401623
X-RAY DIFFRACTIONf_plane_restr0.0049789
X-RAY DIFFRACTIONf_dihedral_angle_d12.37951652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.31931340.25041210X-RAY DIFFRACTION95.79
2.72-2.790.31911410.23981279X-RAY DIFFRACTION100
2.79-2.870.31171390.22841256X-RAY DIFFRACTION100
2.87-2.970.27761420.23011276X-RAY DIFFRACTION99.93
2.97-3.070.29891420.22381293X-RAY DIFFRACTION99.93
3.07-3.190.30391410.20821264X-RAY DIFFRACTION100
3.19-3.340.29921420.20081294X-RAY DIFFRACTION99.93
3.34-3.510.26891420.21021272X-RAY DIFFRACTION100
3.51-3.730.24261420.18011297X-RAY DIFFRACTION99.93
3.73-4.020.18951420.15271279X-RAY DIFFRACTION100
4.02-4.420.20481450.13271312X-RAY DIFFRACTION99.93
4.42-5.050.1731450.13041312X-RAY DIFFRACTION99.93
5.05-6.330.19551470.16141329X-RAY DIFFRACTION99.93
6.33-19.980.20751560.16591404X-RAY DIFFRACTION99.74
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.164688212450.404627907893-0.1380635768383.041275322870.1394149442791.8937883057-0.3039718326950.361844874681-0.215994001136-0.4480893861220.1713941752830.188532381877-0.0351127425715-0.1341756003940.1473376472790.397289414933-0.0990363209112-0.08019864336730.4040263554040.004544823643660.422683998776-21.423003136-15.6452081921.9092507361
20.751831803998-0.2484071737640.8825963059891.41461025271-0.8600494020392.84585781154-0.186090244054-0.01389564515380.1189410214170.1469647812010.02381530699650.031684955462-0.212601255453-0.02738447940610.140463023160.371926330628-0.00163129072831-0.01370272131540.26054615381-0.01231098878110.429590971005-7.43442303331-13.451159653151.7071828943
34.27553865529-3.126833460860.05777238882833.456250279332.018388180913.6195812221-0.73918217421.5652736420.5867394737460.668800182292-0.1895011357010.0224057334366-1.01582760826-0.03552756665650.8655221618340.628524286170.0630372479747-0.0644705658740.9616730764240.06355788180350.671794732526-18.3921820013-19.637350027441.6570801228
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 102 through 323 )AA102 - 3231 - 222
22chain 'A' and (resid 324 through 628 )AA324 - 628223 - 527
33chain 'B' and (resid 1 through 6 )BG1 - 61 - 6

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