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

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Basic information

Entry
Database: PDB / ID: 8ujg
TitleX-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with UDP-GalNAc, Mn2+, and the mono-glycopeptide Srs13.2
Components
  • Glycosyl transferaseGlycosyltransferase
  • SAG-related sequence SRS13
KeywordsTRANSFERASE / GT-A fold GalNAc Glycosyltransferase / Mucin-type O-glycosylation / Toxoplasma gondii cyst wall glycosylation
Function / homology
Function and homology information


polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / carbohydrate binding / Golgi apparatus / membrane
Similarity search - Function
SRS domain superfamily / N-acetylgalactosaminyltransferase / Galactosyltransferase, C-terminal / N-terminal domain of galactosyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / 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 / : / DI(HYDROXYETHYL)ETHER / URIDINE-5'-DIPHOSPHATE / Glycosyl transferase / SAG-related sequence SRS13
Similarity search - Component
Biological speciesToxoplasma gondii ME49 (eukaryote)
Toxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 11, 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: Glycosyl transferase
D: SAG-related sequence SRS13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,38122
Polymers128,9983
Non-polymers2,38219
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.614, 122.624, 165.655
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 99 through 141 or resid 143...
d_2ens_1(chain "B" and (resid 99 through 141 or resid 143...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LEULEUALAALAAA99 - 14127 - 69
d_12GLYGLYARGARGAA143 - 15871 - 86
d_13ALAALAHISHISAA160 - 20088 - 128
d_14VALVALVALVALAA202130
d_15ASNASNPROPROAA204 - 208132 - 136
d_16ILEILEGLUGLUAA210 - 213138 - 141
d_17ILEILELEULEUAA215 - 234143 - 162
d_18GLUGLUGLUGLUAA236 - 251164 - 179
d_19ARGARGILEILEAA253 - 264181 - 192
d_110ALAALAVALVALAA266 - 301194 - 229
d_111PROPROPHEPHEAA303 - 313231 - 241
d_112HISHISHISHISAA315 - 333243 - 261
d_113TYRTYRASPASPAA335 - 375263 - 303
d_114GLYGLYPHEPHEAA377 - 385305 - 313
d_115GLYGLYSERSERAA387 - 421315 - 349
d_116PROPROTHRTHRAA426 - 437354 - 365
d_117LEULEUARGARGAA439 - 456367 - 384
d_118ASNASNARGARGAA458 - 471386 - 399
d_119ARGARGMETMETAA473 - 511401 - 439
d_120LEULEUGLNGLNAA513 - 536441 - 464
d_121PHEPHELYSLYSAA538 - 543466 - 471
d_122GLYGLYPROPROAA545 - 549473 - 477
d_123ASNASNVALVALAA551 - 628479 - 556
d_21LEULEUALAALABB99 - 14127 - 69
d_22GLYGLYARGARGBB143 - 15871 - 86
d_23ALAALAHISHISBB160 - 20088 - 128
d_24VALVALVALVALBB202130
d_25ASNASNPROPROBB204 - 208132 - 136
d_26ILEILEGLUGLUBB210 - 213138 - 141
d_27ILEILELEULEUBB215 - 234143 - 162
d_28GLUGLUGLUGLUBB236 - 251164 - 179
d_29ARGARGILEILEBB253 - 264181 - 192
d_210ALAALAVALVALBB266 - 301194 - 229
d_211PROPROPHEPHEBB303 - 313231 - 241
d_212HISHISHISHISBB315 - 333243 - 261
d_213TYRTYRASPASPBB335 - 375263 - 303
d_214GLYGLYPHEPHEBB377 - 385305 - 313
d_215GLYGLYTHRTHRBB387 - 437315 - 365
d_216LEULEUARGARGBB439 - 456367 - 384
d_217ASNASNARGARGBB458 - 471386 - 399
d_218ARGARGMETMETBB473 - 511401 - 439
d_219LEULEUGLNGLNBB513 - 536441 - 464
d_220PHEPHELYSLYSBB538 - 543466 - 471
d_221GLYGLYPROPROBB545 - 549473 - 477
d_222ASNASNVALVALBB551 - 628479 - 556

NCS oper: (Code: givenMatrix: (0.998804961332, -0.0427503709905, -0.0236865995529), (-0.0436072743762, -0.998366121128, -0.0369255170031), (-0.0220693189674, 0.0379142976282, -0.999037262166)Vector: ...NCS oper: (Code: given
Matrix: (0.998804961332, -0.0427503709905, -0.0236865995529), (-0.0436072743762, -0.998366121128, -0.0369255170031), (-0.0220693189674, 0.0379142976282, -0.999037262166)
Vector: 33.3503523194, -0.711200804321, -2.19157143008)

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Components

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Protein / Protein/peptide / Sugars , 3 types, 4 molecules ABD

#1: Protein Glycosyl transferase / Glycosyltransferase


Mass: 63514.129 Da / Num. of mol.: 2
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 site
Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168
References: UniProt: A0A125YMZ8, polypeptide N-acetylgalactosaminyltransferase
#2: Protein/peptide SAG-related sequence SRS13


Mass: 1970.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Toxoplasma gondii (eukaryote) / References: UniProt: S8F856
#7: 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 , 5 types, 259 molecules

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


Mass: 54.938 Da / Num. of mol.: 4 / 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.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
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: Oct 28, 2022 / Details: CRL single axis focusing system
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: 2.27→30 Å / Num. obs: 62158 / % possible obs: 99.5 % / Redundancy: 7 % / Biso Wilson estimate: 38.55 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.081 / Rrim(I) all: 0.216 / Net I/σ(I): 12
Reflection shellResolution: 2.27→2.34 Å / Rmerge(I) obs: 1.647 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3034 / CC1/2: 0.504 / CC star: 0.818 / Rpim(I) all: 0.682 / Rrim(I) all: 1.787 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SERGUI1.20.1_4487data collection
Aimlessdata scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→29.66 Å / SU ML: 0.3093 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.1194
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2369 3121 5.03 %
Rwork0.1923 58919 -
obs0.1945 62040 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.39 Å2
Refinement stepCycle: LAST / Resolution: 2.27→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8460 0 142 241 8843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00289021
X-RAY DIFFRACTIONf_angle_d0.601312249
X-RAY DIFFRACTIONf_chiral_restr0.04241267
X-RAY DIFFRACTIONf_plane_restr0.00811596
X-RAY DIFFRACTIONf_dihedral_angle_d14.35293352
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.817553700325 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.310.3336960.29751936X-RAY DIFFRACTION71.83
2.31-2.350.3441530.28112665X-RAY DIFFRACTION99.89
2.35-2.390.30221300.2732701X-RAY DIFFRACTION99.68
2.39-2.430.3111400.26132686X-RAY DIFFRACTION99.96
2.43-2.480.33411560.25042699X-RAY DIFFRACTION99.86
2.48-2.530.25941500.25792644X-RAY DIFFRACTION99.96
2.53-2.580.3161460.25232715X-RAY DIFFRACTION99.76
2.58-2.640.31511330.23852693X-RAY DIFFRACTION99.93
2.64-2.710.3071490.23962688X-RAY DIFFRACTION100
2.71-2.780.26391250.22112745X-RAY DIFFRACTION99.97
2.78-2.860.26741530.21352628X-RAY DIFFRACTION98.62
2.86-2.960.27531480.22262695X-RAY DIFFRACTION99.27
2.96-3.060.24711460.21912699X-RAY DIFFRACTION99.96
3.06-3.190.33261530.21732731X-RAY DIFFRACTION99.86
3.19-3.330.27751470.19882724X-RAY DIFFRACTION99.9
3.33-3.510.26491450.19812715X-RAY DIFFRACTION99.9
3.51-3.720.22961300.18872737X-RAY DIFFRACTION99.79
3.72-4.010.18451360.15852729X-RAY DIFFRACTION99.51
4.01-4.410.16141420.1352693X-RAY DIFFRACTION97.42
4.41-5.050.17611350.13112764X-RAY DIFFRACTION99.52
5.05-6.350.1861560.1652792X-RAY DIFFRACTION99.43
6.35-29.660.19721520.18252840X-RAY DIFFRACTION96.89
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)
11.93823130251-0.533982956578-0.07483311697862.491773143810.2135980173631.734813670560.10742540360.3653665717860.0573108424861-0.281022004233-0.2622446694410.1039133648210.002354742274860.005308308395380.1445956164940.297753878450.07281799966670.004730622635930.3094717304710.02741207091230.296006670596-17.465356242521.8042531057-21.8464507032
20.182618022889-0.20672805956-0.08208402572280.997969672934-0.3495410023491.445122163640.0312870115053-0.03907618369740.06461385148260.0546961861123-0.106064308915-0.1510257561210.03184256586170.1270890282940.08217480471350.222267567120.00398969541303-0.01155874423050.2968629688910.03292791258950.324002362645-9.0902361853616.7038710077-3.84409725324
31.656102513430.162346997649-1.022469537630.562599366144-0.7092535504592.5923788337-0.00989612789121-0.3073990671530.04259650209930.00676302489675-0.119829543363-0.04299072932990.175765814380.1860702071070.1075978122970.2876811791680.00750082546681-0.03768882501870.3204195032390.005811926731670.317251052816-16.44914468392.6781493909516.2362751255
41.652959150940.260212300522-0.4465569895860.676156148699-0.7058004459581.300292912470.141362973354-0.3359757262550.01855628463260.190499190123-0.197765688663-0.000760548605461-0.04811631213580.1809548099530.04658617289640.406106354011-0.08514424245770.02734691828130.301283411732-0.01682069412920.27434905090819.3302962974-19.414541010913.6586885169
51.187916941-0.4122690707850.6654377303170.160418885653-0.9186354166211.957966952890.03787805469760.0430992177090.188946169857-0.0497774405215-0.100566249566-0.01034659999550.133450759526-0.02639894871710.04724242913020.2381437500280.000216547234310.01537787695490.254840080157-0.03011930448220.30401762774316.5033049121-4.27321310455-15.9846917959
62.384931696493.106790945691.712820480624.047124022172.201573024015.210064900990.220640873781-0.4511044986250.09864553573540.454601187216-0.1955785192690.07362189178550.01294167299060.0699434205168-0.006117266815011.11940048161-0.2739242745920.1618918352990.8246627214740.03913178307971.11029605819-20.384616131817.8900806509-0.486159272805
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 99 through 286 )AA99 - 2861 - 188
22chain 'A' and (resid 287 through 428 )AA287 - 428189 - 330
33chain 'A' and (resid 429 through 628 )AA429 - 628331 - 530
44chain 'B' and (resid 98 through 402 )BB98 - 4021 - 305
55chain 'B' and (resid 403 through 635 )BB403 - 635306 - 530
66chain 'D' and (resid 2 through 3 )DH2 - 31 - 2

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