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- PDB-5o5e: Crystal structure of human UDP-N-acetylglucosamine-dolichyl-phosp... -

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Basic information

Entry
Database: PDB / ID: 5o5e
TitleCrystal structure of human UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) (V264G mutant) in complex with tunicamycin
ComponentsUDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
KeywordsTRANSFERASE / Protein glycosylation / integral membrane protein / PNPT / congenital myasthenic syndrome / antibiotic / Structural Genomics / Structural Genomics Consortium / SGC
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
Tunicamycin / Chem-P6L / Unknown ligand / UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsPike, A.C.W. / Dong, Y.Y. / Chu, A. / Tessitore, A. / Goubin, S. / Dong, L. / Mukhopadhyay, S. / Mahajan, P. / Chalk, R. / Berridge, G. ...Pike, A.C.W. / Dong, Y.Y. / Chu, A. / Tessitore, A. / Goubin, S. / Dong, L. / Mukhopadhyay, S. / Mahajan, P. / Chalk, R. / Berridge, G. / Wang, D. / Kupinska, K. / Belaya, K. / Beeson, D. / Burgess-Brown, N. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Cell / Year: 2018
Title: Structures of DPAGT1 Explain Glycosylation Disease Mechanisms and Advance TB Antibiotic Design.
Authors: Dong, Y.Y. / Wang, H. / Pike, A.C.W. / Cochrane, S.A. / Hamedzadeh, S. / Wyszynski, F.J. / Bushell, S.R. / Royer, S.F. / Widdick, D.A. / Sajid, A. / Boshoff, H.I. / Park, Y. / Lucas, R. / ...Authors: Dong, Y.Y. / Wang, H. / Pike, A.C.W. / Cochrane, S.A. / Hamedzadeh, S. / Wyszynski, F.J. / Bushell, S.R. / Royer, S.F. / Widdick, D.A. / Sajid, A. / Boshoff, H.I. / Park, Y. / Lucas, R. / Liu, W.M. / Lee, S.S. / Machida, T. / Minall, L. / Mehmood, S. / Belaya, K. / Liu, W.W. / Chu, A. / Shrestha, L. / Mukhopadhyay, S.M.M. / Strain-Damerell, C. / Chalk, R. / Burgess-Brown, N.A. / Bibb, M.J. / Barry Iii, C.E. / Robinson, C.V. / Beeson, D. / Davis, B.G. / Carpenter, E.P.
History
DepositionJun 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2164
Polymers46,1741
Non-polymers3,0423
Water1629
1
A: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
hetero molecules

A: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4318
Polymers92,3472
Non-polymers6,0846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area6450 Å2
ΔGint-79 kcal/mol
Surface area31390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.091, 102.091, 240.061
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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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: 46173.719 Da / Num. of mol.: 1 / Mutation: V264G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPAGT1, DPAGT2 / Plasmid: PFB-LIC-BSE / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9H3H5, UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase
#2: Chemical ChemComp-P6L / (2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE


Mass: 746.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H75O10P / Comment: phospholipid*YM
#3: Chemical ChemComp-9LH / Tunicamycin / Tunicamycin


Mass: 830.916 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H62N4O16 / Comment: antibiotic*YM
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 3.91 Å3/Da / Density % sol: 68.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M bicine pH 8.5 -- 0.05M sodium chloride -- 36% PEG200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.4→59.33 Å / Num. obs: 10832 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 131 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.032 / Net I/σ(I): 13.4
Reflection shellResolution: 3.4→3.49 Å / Redundancy: 9.8 % / Rmerge(I) obs: 2.295 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 761 / CC1/2: 0.435 / Rpim(I) all: 1.044 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimless0.5.25data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→25.87 Å / Cor.coef. Fo:Fc: 0.9076 / Cor.coef. Fo:Fc free: 0.9298 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.428
Details: STRUCTURE REFINED WITH BUSTER WITH A SINGLE TLS GROUP. ELECTRON DENSITY MAPS WERE SHARPENED WITH -100A**2 BFACTOR FOR REBUILDING IN COOT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 552 5.12 %RANDOM
Rwork0.2294 ---
obs0.2298 10786 99.9 %-
Displacement parametersBiso mean: 172.25 Å2
Baniso -1Baniso -2Baniso -3
1--5.492 Å20 Å20 Å2
2---5.492 Å20 Å2
3---10.9839 Å2
Refine analyzeLuzzati coordinate error obs: 0.439 Å
Refinement stepCycle: 1 / Resolution: 3.4→25.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 104 9 3050
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093117HARMONIC2
X-RAY DIFFRACTIONt_angle_deg14238HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1399SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes43HARMONIC2
X-RAY DIFFRACTIONt_gen_planes451HARMONIC5
X-RAY DIFFRACTIONt_it3117HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.22
X-RAY DIFFRACTIONt_other_torsion3.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion424SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3888SEMIHARMONIC4
LS refinement shellResolution: 3.4→3.8 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2602 147 4.94 %
Rwork0.2095 2826 -
all0.2118 2973 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: 45.6838 Å / Origin y: 49.8451 Å / Origin z: 128.728 Å
111213212223313233
T-0.6971 Å2-0.1107 Å2-0.0373 Å2-0.2511 Å20.2447 Å2---0.4151 Å2
L4.2871 °20.9869 °2-0.6794 °2-6.0762 °2-0.5503 °2--4.0734 °2
S-0.2455 Å °1.0588 Å °0.6805 Å °-0.2991 Å °0.2782 Å °-0.4952 Å °-0.3093 Å °1.1035 Å °-0.0327 Å °
Refinement TLS groupSelection details: {A|8 - 402}

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