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- PDB-6bw6: Human GPT (DPAGT1) H129 variant in complex with tunicamycin -

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Basic information

Entry
Database: PDB / ID: 6bw6
TitleHuman GPT (DPAGT1) H129 variant in complex with tunicamycin
ComponentsUDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
KeywordsTRANSFERASE/ANTIBIOTIC / N-linked glycosylation / endoplasmic reticulum / tunicamycin / natural product / TRANSFERASE / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein / Defective DPAGT1 causes CDG-1j, CMSTA2 / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / dolichol-linked oligosaccharide biosynthetic process / UDP-N-acetylglucosamine metabolic process / protein N-linked glycosylation / glycosyltransferase activity / intracellular membrane-bounded organelle ...Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein / Defective DPAGT1 causes CDG-1j, CMSTA2 / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / dolichol-linked oligosaccharide biosynthetic process / UDP-N-acetylglucosamine metabolic process / protein N-linked glycosylation / glycosyltransferase activity / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / membrane / identical protein binding / metal ion binding
Similarity search - Function
: / DPAGT1 insertion domain / UDP-GlcNAc-dolichyl-phosphate GlcNAc phosphotransferase / Glycosyl transferase, family 4 / Glycosyl transferase family 4
Similarity search - Domain/homology
Chem-PGW / Tunicamycin / UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsYoo, J. / Kuk, A.C.Y. / Mashalidis, E.H. / Lee, S.-Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120594 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35NS097241 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: GlcNAc-1-P-transferase-tunicamycin complex structure reveals basis for inhibition of N-glycosylation.
Authors: Yoo, J. / Mashalidis, E.H. / Kuk, A.C.Y. / Yamamoto, K. / Kaeser, B. / Ichikawa, S. / Lee, S.Y.
History
DepositionDec 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
B: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
C: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
D: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,07112
Polymers188,8084
Non-polymers6,2648
Water0
1
A: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
B: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5366
Polymers94,4042
Non-polymers3,1324
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-55 kcal/mol
Surface area28570 Å2
MethodPISA
2
C: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
D: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5366
Polymers94,4042
Non-polymers3,1324
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-60 kcal/mol
Surface area28030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.615, 105.363, 148.080
Angle α, β, γ (deg.)90.00, 103.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase / GlcNAc-1-P transferase / GPT / N-acetylglucosamine-1-phosphate transferase


Mass: 47201.891 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPAGT1, DPAGT2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9H3H5, UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase
#2: Chemical
ChemComp-TUM / Tunicamycin / Tunicamycin


Mass: 816.889 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C37H60N4O16 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical
ChemComp-PGW / (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate / 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)] / PHOSPHATIDYLGLYCEROL / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM

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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: 4.33 Å3/Da / Density % sol: 71.56 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: PEG400, calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.95→100 Å / Num. obs: 36769 / % possible obs: 92.58 % / Redundancy: 112.4 % / CC1/2: 0.84 / Rpim(I) all: 0.07883 / Net I/σ(I): 17.51
Reflection shellResolution: 2.95→3.055 Å / Redundancy: 112.8 % / Num. unique obs: 6360 / CC1/2: 0.763 / % possible all: 54.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LEV

5lev


Resolution: 2.95→94.509 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.14
RfactorNum. reflection% reflection
Rfree0.2908 1831 4.98 %
Rwork0.2599 --
obs0.2614 36769 55.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.95→94.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11280 0 364 0 11644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311942
X-RAY DIFFRACTIONf_angle_d0.57616281
X-RAY DIFFRACTIONf_dihedral_angle_d10.0216776
X-RAY DIFFRACTIONf_chiral_restr0.0392013
X-RAY DIFFRACTIONf_plane_restr0.0041952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.02980.3976340.3871754X-RAY DIFFRACTION16
3.0298-3.1190.3626360.3545810X-RAY DIFFRACTION17
3.119-3.21960.4297480.3322883X-RAY DIFFRACTION18
3.2196-3.33470.3916650.31831016X-RAY DIFFRACTION21
3.3347-3.46820.3783630.36951249X-RAY DIFFRACTION26
3.4682-3.62610.3411730.31231606X-RAY DIFFRACTION33
3.6261-3.81730.30341060.29782109X-RAY DIFFRACTION44
3.8173-4.05640.30991630.24992865X-RAY DIFFRACTION59
4.0564-4.36960.29182060.23484135X-RAY DIFFRACTION85
4.3696-4.80940.26972600.21944772X-RAY DIFFRACTION98
4.8094-5.50520.25112590.23154839X-RAY DIFFRACTION100
5.5052-6.93570.31632500.2914919X-RAY DIFFRACTION100
6.9357-94.55760.27322680.27084981X-RAY DIFFRACTION100

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