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- PDB-6fm9: Crystal structure of human UDP-N-acetylglucosamine-dolichyl-phosp... -

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Basic information

Entry
Database: PDB / ID: 6fm9
TitleCrystal structure of human UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1)
ComponentsUDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
KeywordsTRANSFERASE / Protein glycosylation / integral membrane protein / congenital myasthenic syndrome 13 / 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
Chem-P6L / UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 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 Trust106169/Z/14/Z 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
DepositionJan 30, 2018Deposition 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 1.2Jan 17, 2024Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,9632
Polymers46,2161
Non-polymers7471
Water0
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)93,9264
Polymers92,4322
Non-polymers1,4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area4870 Å2
ΔGint-67 kcal/mol
Surface area32590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.799, 103.799, 241.099
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: 46215.797 Da / Num. of mol.: 1
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

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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: 4.06 Å3/Da / Density % sol: 69.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.05M ADA pH 6.5 -- 24% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 3.6→72.06 Å / Num. obs: 9509 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 99.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.024 / Rrim(I) all: 0.061 / Net I/σ(I): 17.8
Reflection shellResolution: 3.6→3.69 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.132 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 681 / CC1/2: 0.666 / Rpim(I) all: 0.475 / Rrim(I) all: 1.23 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDS3-NOV-2014data reduction
Aimless0.5.1data scaling
MR-Rosettaphasing
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J72

4j72


Resolution: 3.6→30 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.538
Details: Refined using 5LEV as target reference restraints. Single TLS group for entire protein chain.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 479 5.08 %RANDOM
Rwork0.249 ---
obs0.25 9435 99.4 %-
Displacement parametersBiso mean: 171.41 Å2
Baniso -1Baniso -2Baniso -3
1--2.0005 Å20 Å20 Å2
2---2.0005 Å20 Å2
3---4.001 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: 1 / Resolution: 3.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 25 0 2865
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092931HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.033996HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d940SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes480HARMONIC5
X-RAY DIFFRACTIONt_it2931HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2
X-RAY DIFFRACTIONt_other_torsion19.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion402SEMIHARMONIC5
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_contact3476SEMIHARMONIC4
LS refinement shellResolution: 3.6→4.03 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2265 126 4.84 %
Rwork0.216 2477 -
all0.2165 2603 -
obs--99.58 %
Refinement TLS params.Method: refined / Origin x: 47.2354 Å / Origin y: 50.461 Å / Origin z: 129.432 Å
111213212223313233
T-0.4769 Å2-0.1167 Å20.0775 Å2-0.1321 Å20.1557 Å2---0.3719 Å2
L4.7918 °22.0834 °2-0.9846 °2-6.3738 °2-0.2978 °2--4.1493 °2
S-0.2653 Å °0.8051 Å °0.6731 Å °-0.598 Å °0.4891 Å °-0.525 Å °-0.3755 Å °0.9249 Å °-0.2238 Å °
Refinement TLS groupSelection details: { A|7 - A|405 }

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