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- PDB-6iwr: Crystal structure of GalNAc-T7 with UDP, GalNAc and Mn2+ -

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Basic information

Entry
Database: PDB / ID: 6iwr
TitleCrystal structure of GalNAc-T7 with UDP, GalNAc and Mn2+
ComponentsN-acetylgalactosaminyltransferase 7
KeywordsTRANSFERASE / Polypeptide N Acetylgalactosaminyltransferase Activity / Transferring Glycosyl Groups / Manganese Ion Binding / Carbohydrate Binding / Metal Ion Binding
Function / homology
Function and homology information


polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via N-acetyl-galactosamine / O-linked glycosylation of mucins / protein O-linked glycosylation / carbohydrate binding / carbohydrate metabolic process / Golgi membrane / Golgi apparatus / extracellular exosome ...polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via N-acetyl-galactosamine / O-linked glycosylation of mucins / protein O-linked glycosylation / carbohydrate binding / carbohydrate metabolic process / Golgi membrane / Golgi apparatus / extracellular exosome / metal ion binding / membrane
Similarity search - Function
N-acetylgalactosaminyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A ...N-acetylgalactosaminyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / URIDINE-5'-DIPHOSPHATE / N-acetylgalactosaminyltransferase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.604 Å
AuthorsYu, C. / Yin, Y.X.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Structural basis of carbohydrate transfer activity of UDP-GalNAc: Polypeptide N-acetylgalactosaminyltransferase 7.
Authors: Yu, C. / Liang, L. / Yin, Y.
History
DepositionDec 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylgalactosaminyltransferase 7
B: N-acetylgalactosaminyltransferase 7
C: N-acetylgalactosaminyltransferase 7
D: N-acetylgalactosaminyltransferase 7
E: N-acetylgalactosaminyltransferase 7
F: N-acetylgalactosaminyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)414,74815
Polymers413,1856
Non-polymers1,5629
Water7,332407
1
A: N-acetylgalactosaminyltransferase 7
B: N-acetylgalactosaminyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,8384
Polymers137,7282
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-23 kcal/mol
Surface area46730 Å2
MethodPISA
2
C: N-acetylgalactosaminyltransferase 7
D: N-acetylgalactosaminyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,0717
Polymers137,7282
Non-polymers1,3435
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-36 kcal/mol
Surface area46310 Å2
MethodPISA
3
E: N-acetylgalactosaminyltransferase 7
hetero molecules

F: N-acetylgalactosaminyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,8384
Polymers137,7282
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y+1/2,-z-1/21
Buried area1990 Å2
ΔGint-27 kcal/mol
Surface area46680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.435, 158.264, 251.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 7 molecules ABCDEF

#1: Protein
N-acetylgalactosaminyltransferase 7 / Polypeptide GalNAc transferase 7 / pp-GaNTase 7 / Protein-UDP acetylgalactosaminyltransferase 7 / ...Polypeptide GalNAc transferase 7 / pp-GaNTase 7 / Protein-UDP acetylgalactosaminyltransferase 7 / UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 7


Mass: 68864.211 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GALNT7 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q86SF2, Transferases; Glycosyltransferases; Hexosyltransferases
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 415 molecules

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


Mass: 54.938 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: Mn
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical ChemComp-UD2 / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / (2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.31 Å3/Da / Density % sol: 62.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Lithium sulfate monohydrate, 12%(w/v) Polyethylene glycol 4,000, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 5mM UDP, 5mM MnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.604→49.251 Å / Num. obs: 160537 / % possible obs: 96 % / Redundancy: 6.7 % / Net I/σ(I): 12.75
Reflection shellResolution: 2.604→2.697 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2400: ???)refinement
DENZOdata reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.604→49.251 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.55
RfactorNum. reflection% reflection
Rfree0.258 8023 5 %
Rwork0.2201 --
obs0.222 160475 95.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.604→49.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26580 0 85 407 27072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01127461
X-RAY DIFFRACTIONf_angle_d1.29937241
X-RAY DIFFRACTIONf_dihedral_angle_d2610297
X-RAY DIFFRACTIONf_chiral_restr0.0763833
X-RAY DIFFRACTIONf_plane_restr0.0074790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6038-2.63340.35491990.30663404X-RAY DIFFRACTION65
2.6334-2.66440.35731900.30943749X-RAY DIFFRACTION71
2.6644-2.69690.33462110.30384010X-RAY DIFFRACTION76
2.6969-2.7310.35132210.28594394X-RAY DIFFRACTION83
2.731-2.7670.33042330.28294644X-RAY DIFFRACTION89
2.767-2.80490.31182510.2774979X-RAY DIFFRACTION94
2.8049-2.84490.3352660.27745088X-RAY DIFFRACTION97
2.8449-2.88740.29192850.27815192X-RAY DIFFRACTION99
2.8874-2.93250.31352900.28155216X-RAY DIFFRACTION99
2.9325-2.98060.33862680.28145249X-RAY DIFFRACTION100
2.9806-3.0320.33542900.28045263X-RAY DIFFRACTION100
3.032-3.08710.31422850.28355259X-RAY DIFFRACTION100
3.0871-3.14650.36442810.29765273X-RAY DIFFRACTION100
3.1465-3.21070.35222740.28665291X-RAY DIFFRACTION100
3.2107-3.28050.33262790.27075286X-RAY DIFFRACTION100
3.2805-3.35680.30712970.2595255X-RAY DIFFRACTION100
3.3568-3.44070.28242740.24965302X-RAY DIFFRACTION100
3.4407-3.53370.28742830.24955269X-RAY DIFFRACTION100
3.5337-3.63760.28592950.23945280X-RAY DIFFRACTION100
3.6376-3.7550.25792690.21975291X-RAY DIFFRACTION100
3.755-3.88920.2312630.20085326X-RAY DIFFRACTION100
3.8892-4.04480.2072790.19325344X-RAY DIFFRACTION100
4.0448-4.22880.21842720.18345286X-RAY DIFFRACTION100
4.2288-4.45160.19543090.16035305X-RAY DIFFRACTION100
4.4516-4.73030.20142540.15495385X-RAY DIFFRACTION100
4.7303-5.09520.18762860.16395344X-RAY DIFFRACTION100
5.0952-5.60730.20012800.18165362X-RAY DIFFRACTION100
5.6073-6.41720.24152700.20725397X-RAY DIFFRACTION100
6.4172-8.07920.2452820.19565448X-RAY DIFFRACTION100
8.0792-49.25970.19642870.17685561X-RAY DIFFRACTION98

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