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- PDB-7sj2: N-acetylglucosamine-1-phosphotransferase (GNPT) alpha and beta su... -

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Basic information

Entry
Database: PDB / ID: 7sj2
TitleN-acetylglucosamine-1-phosphotransferase (GNPT) alpha and beta subunits (GNPTAB) catalytic domain, from zebrafish, in complex with uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) and magnesium
ComponentsN-acetylglucosamine-1-phosphotransferase subunit alpha,N-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 / protein N-linked glycosylation via asparagine / embryonic cranial skeleton morphogenesis / cartilage development / lysosome organization ...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 / protein N-linked glycosylation via asparagine / embryonic cranial skeleton morphogenesis / cartilage development / lysosome organization / heart morphogenesis / bone development / Golgi membrane / calcium ion binding / Golgi apparatus / metal ion binding / membrane
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
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / LNR domain-containing protein / N-acetylglucosamine-1-phosphotransferase subunits alpha/beta
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Dictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionOct 15, 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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)122,00919
Polymers116,7262
Non-polymers5,28317
Water13,836768
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13030 Å2
ΔGint-31 kcal/mol
Surface area43010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.542, 87.142, 108.369
Angle α, β, γ (deg.)90.000, 111.858, 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 subunit alpha,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. exp.) Dictyostelium discoideum (eukaryote)
Gene: gnptab, gnpta, si:ch211-234f20.3, zgc:122985, DDB0186697
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5RGJ8, UniProt: Q54MP1

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Sugars , 5 types, 9 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: 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.: 2
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
#4: 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
#5: 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
#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.: 4 / 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 , 4 types, 776 molecules

#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 768 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.55 Å3/Da / Density % sol: 65.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystallized in PEG 5000 MME, Tris pH 8.5. Soaked in PEG 3350, Tris 7.5, UDP-GlcNAc and MgCl2. Cryoprotected with glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 66254 / % possible obs: 91 % / Redundancy: 6.9 % / Biso Wilson estimate: 30.09 Å2 / CC1/2: 1 / Net I/σ(I): 39.1
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 2852 / CC1/2: 0.83

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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: 7S6N

7s6n


Resolution: 2.3→47.42 Å / SU ML: 0.2137 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.4499
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2018 1971 2.97 %
Rwork0.1604 64282 -
obs0.1616 66253 91.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.76 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7174 0 340 768 8282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317695
X-RAY DIFFRACTIONf_angle_d0.614710435
X-RAY DIFFRACTIONf_chiral_restr0.05041199
X-RAY DIFFRACTIONf_plane_restr0.00481305
X-RAY DIFFRACTIONf_dihedral_angle_d13.40632911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.2656510.25781668X-RAY DIFFRACTION33.25
2.36-2.420.2558980.20873181X-RAY DIFFRACTION63.69
2.42-2.490.22631270.19754328X-RAY DIFFRACTION86.44
2.49-2.570.23651500.184936X-RAY DIFFRACTION97.75
2.57-2.660.22841580.17684949X-RAY DIFFRACTION99.51
2.66-2.770.21771540.1734986X-RAY DIFFRACTION99.25
2.77-2.90.21471520.15634970X-RAY DIFFRACTION98.99
2.9-3.050.21441520.15424983X-RAY DIFFRACTION98.85
3.05-3.240.21751560.16045005X-RAY DIFFRACTION100
3.24-3.490.20621560.15825069X-RAY DIFFRACTION99.87
3.49-3.840.16661520.13714986X-RAY DIFFRACTION99.54
3.84-4.40.17181530.12095006X-RAY DIFFRACTION98.74
4.4-5.540.15921530.14425088X-RAY DIFFRACTION99.98
5.54-47.420.2341590.19915127X-RAY DIFFRACTION99.19
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)
11.146399453170.971437864468-0.1655437701882.60322407957-1.570093238762.023663597520.14672259119-0.0250239214495-0.0131588796862-0.116337149976-0.146961765013-0.0954749411209-0.241928427190.291911305859-0.1843625382780.109240096119-0.03623387213750.01811181573690.142314584744-0.0654871119770.27124624491738.07052758999.278625426727.66656730168
22.0487809289-0.130301084796-1.255279300953.61564582282-1.359036816984.386060413720.092632627917-0.30732403999-0.000734937880054-0.22636348911-0.186369704043-0.2099763179390.1494702309070.681136160511-0.09779488659080.0333525636437-0.0311009618664-0.02440865786450.101142194854-0.06653046690680.13698662413141.33617902473.268456637036.36611111135
31.92863144339-0.0392976446355-0.8530412225891.067658711990.2715784639770.604152768877-0.0932927699446-0.402718935116-0.5195864602760.247104725566-0.577482058348-0.2947100911140.2353411835130.731296970105-0.251405237380.6385201319750.0658744867666-0.07492179514630.6308704567330.194401428420.27832873835742.5283958942-24.878206825840.4790493542
40.697709999689-0.2567113614380.1179464601832.62673184139-1.893790761092.08989188543-0.0328886070607-0.699985246837-0.0856511120730.298004439114-0.261357187457-0.3137419523630.354418837410.3425155946330.08054953312230.4590819097050.0713229268432-0.006954422705430.7522169045480.1585956899370.40691259850344.8991434431-20.027937081235.4972398681
53.01817723578-0.1002472496020.06638006858532.11906219408-0.1858422269262.034723921640.1755946388610.7112514272670.0130742699928-0.756592282754-0.02688478438590.285815985121-0.195323988425-0.3752377339910.3318272289570.3982259611470.040234099625-0.1186290943530.293673661095-0.01115936543880.28396174054224.03397848378.84153406694-9.97678708872
60.87076394904-0.2325711084530.197726576181.47464407105-0.3587144637383.138167718440.53079018541-0.35624821810.1223410975020.887013886404-0.1872567254160.344009738814-0.147695063035-0.305951476668-0.1310989626090.460330421851-0.1191178940240.1290147656510.332518032101-0.1146798968840.20302698193313.9292667294-2.4208323433237.6389153386
73.412127105010.657989936-0.1759657137032.78491385384-0.1813672668624.034279425010.341501401755-0.157324534483-0.1420494184810.519747131232-0.1850619702690.5998261592820.304245162586-0.4918736790070.02154872941160.327020743211-0.1365623174580.08176252235720.24753253969-0.08953360149990.2665929709547.59627627644-11.318690563435.9477223942
81.93903106529-0.378075511309-0.4197412459521.4807134225-1.303811318012.30292300130.2185345138570.309701175093-0.160416772516-0.03393354974440.183075956110.1394050504890.216173701189-0.555746758852-0.399752479390.2879289927640.0211067640057-0.1723743697610.4604975322060.07051389823380.4793457784448.267551175738.41128331384-1.31839835051
90.749213970693-0.353982979830.6004213713681.76779885279-0.5989639545162.706127917330.2717470993970.349462731495-0.206336617138-0.1698935733080.3207471285231.420906031380.54552181641-2.018698029720.3282433633490.1408380045880.182439821329-0.2799170859190.8966078328830.3442353378820.693029994439-0.029178679628212.8349639881-7.31545869396
102.793319669330.253034776777-0.3793763776542.60630754432-0.4355357355831.736721594090.255471794146-0.545769451867-0.5569925525080.790119216844-0.2793076475120.2879774290850.4315622948920.04158590067760.2311673120560.609647745192-0.1821477040930.04346762281650.4532536124280.01951951005160.2508409466217.607181377-17.556285651544.6439340477
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 56 through 138 )AA56 - 1381 - 62
22chain 'A' and (resid 139 through 323 )AA139 - 32363 - 241
33chain 'A' and (resid 324 through 380 )AA324 - 380242 - 298
44chain 'A' and (resid 381 through 440 )AA381 - 440299 - 352
55chain 'A' and (resid 441 through 525 )AA441 - 525353 - 428
66chain 'B' and (resid 56 through 103 )BN56 - 1031 - 48
77chain 'B' and (resid 104 through 323 )BN104 - 32349 - 238
88chain 'B' and (resid 324 through 363 )BN324 - 363239 - 278
99chain 'B' and (resid 364 through 425 )BN364 - 425279 - 336
1010chain 'B' and (resid 426 through 528 )BN426 - 528337 - 439

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