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- PDB-7s6n: N-acetylglucosamine-1-phosphotransferase (GNPT) alpha and beta su... -

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Basic information

Entry
Database: PDB / ID: 7s6n
TitleN-acetylglucosamine-1-phosphotransferase (GNPT) alpha and beta subunits (GNPTAB) catalytic domain, from zebrafish
ComponentsN-acetylglucosamine-1-phosphotransferase (GNPT) alpha (GNPTAB) catalytic domain,N-acetylglucosamine-1-phosphotransferase subunit beta
KeywordsTRANSFERASE / GNPT / lysosome / mannose 6-phosphate / mucolipidosis
Function / homology
Function and homology information


UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase / N-glycan processing to lysosome / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / chondrocyte development / embryonic viscerocranium morphogenesis / carbohydrate phosphorylation / embryonic cranial skeleton morphogenesis / cartilage development / lysosome organization / heart morphogenesis ...UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase / N-glycan processing to lysosome / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / chondrocyte development / embryonic viscerocranium morphogenesis / carbohydrate phosphorylation / embryonic cranial skeleton morphogenesis / cartilage development / lysosome organization / heart morphogenesis / bone development / Golgi membrane / calcium ion binding / Golgi apparatus
Similarity search - Function
N-acetylglucosamine-1-phosphotransferase subunit alpha/beta, regulatory domain / Putative GlcNAc-1 phosphotransferase regulatory domain / Stealth protein CR2, conserved region 2 / Stealth protein CR4, conserved region 4 / Stealth protein CR3, conserved region 3 / Stealth protein CR1, conserved region 1 / : / Stealth protein CR2, conserved region 2 / Stealth protein CR1, conserved region 1 / Stealth protein CR3, conserved region 3 ...N-acetylglucosamine-1-phosphotransferase subunit alpha/beta, regulatory domain / Putative GlcNAc-1 phosphotransferase regulatory domain / Stealth protein CR2, conserved region 2 / Stealth protein CR4, conserved region 4 / Stealth protein CR3, conserved region 3 / Stealth protein CR1, conserved region 1 / : / Stealth protein CR2, conserved region 2 / Stealth protein CR1, conserved region 1 / Stealth protein CR3, conserved region 3 / Stealth protein CR4, conserved region 4 / DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / Notch-like domain superfamily / LNR domain / LNR (Lin-12/Notch) repeat profile. / Notch domain / Domain found in Notch and Lin-12 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain
Similarity search - Domain/homology
N-acetylglucosamine-1-phosphotransferase subunits alpha/beta
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGorelik, A. / Illes, K. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-173264 Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structures of the mannose-6-phosphate pathway enzyme, GlcNAc-1-phosphotransferase.
Authors: Gorelik, A. / Illes, K. / Bui, K.H. / Nagar, B.
History
DepositionSep 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylglucosamine-1-phosphotransferase (GNPT) alpha (GNPTAB) catalytic domain,N-acetylglucosamine-1-phosphotransferase subunit beta
B: N-acetylglucosamine-1-phosphotransferase (GNPT) alpha (GNPTAB) catalytic domain,N-acetylglucosamine-1-phosphotransferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,18513
Polymers116,7262
Non-polymers3,45911
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint14 kcal/mol
Surface area44200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.182, 86.605, 106.985
Angle α, β, γ (deg.)90.000, 112.169, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein N-acetylglucosamine-1-phosphotransferase (GNPT) alpha (GNPTAB) catalytic domain,N-acetylglucosamine-1-phosphotransferase subunit beta


Mass: 58363.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: gnptab, gnpta, si:ch211-234f20.3, zgc:122985 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5RGJ8

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Sugars , 5 types, 9 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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.: 5 / Source method: obtained synthetically / 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 , 2 types, 380 molecules

#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.57 Å3/Da / Density % sol: 65.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% PEG3350, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 63354 / % possible obs: 90.53 % / Redundancy: 6.6 % / Biso Wilson estimate: 37.39 Å2 / Rrim(I) all: 0.115 / Net I/σ(I): 16.5
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 4471 / CC1/2: 0.435

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold-2

Resolution: 2.7→48.42 Å / SU ML: 0.3011 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4454
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2307 2996 4.73 %
Rwork0.1835 60358 -
obs0.1858 63354 71.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.95 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7175 0 223 378 7776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00537589
X-RAY DIFFRACTIONf_angle_d0.641710292
X-RAY DIFFRACTIONf_chiral_restr0.04471167
X-RAY DIFFRACTIONf_plane_restr0.00551306
X-RAY DIFFRACTIONf_dihedral_angle_d12.59872874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.3211370.3205723X-RAY DIFFRACTION18.25
2.74-2.790.3826490.28211014X-RAY DIFFRACTION25.15
2.79-2.840.3483700.29551252X-RAY DIFFRACTION31.52
2.84-2.90.3011860.27011627X-RAY DIFFRACTION40.02
2.9-2.960.3052890.25051864X-RAY DIFFRACTION46.47
2.96-3.020.2873990.24532061X-RAY DIFFRACTION51.18
3.02-3.090.28921130.23962238X-RAY DIFFRACTION55.4
3.09-3.170.28741200.21892409X-RAY DIFFRACTION60.31
3.17-3.250.23861300.20232680X-RAY DIFFRACTION65.82
3.25-3.350.241450.1972863X-RAY DIFFRACTION70.81
3.35-3.460.24671550.20013073X-RAY DIFFRACTION76.44
3.46-3.580.32191320.18783136X-RAY DIFFRACTION78.52
3.58-3.720.2041940.16963747X-RAY DIFFRACTION92.58
3.72-3.890.20111910.15693690X-RAY DIFFRACTION92.71
3.89-4.10.19681990.14673974X-RAY DIFFRACTION98.28
4.1-4.360.17651990.12993993X-RAY DIFFRACTION99.38
4.36-4.690.1812000.13623990X-RAY DIFFRACTION99.64
4.69-5.160.21371990.14724034X-RAY DIFFRACTION99.62
5.16-5.910.21042040.19083992X-RAY DIFFRACTION99.41
5.91-7.440.26041880.21944008X-RAY DIFFRACTION99.55
7.44-48.420.25791970.21563990X-RAY DIFFRACTION98.87

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