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- PDB-9f5h: Crystal structure of MGAT5 bump-and-hole mutant in complex with U... -

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Basic information

Entry
Database: PDB / ID: 9f5h
TitleCrystal structure of MGAT5 bump-and-hole mutant in complex with UDP and M592
ComponentsSecreted alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
KeywordsTRANSFERASE / Bump and hole / bioorthogonal tag
Function / homology
Function and homology information


alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase / alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity / N-Glycan antennae elongation / positive regulation of receptor signaling pathway via STAT / : / protein N-linked glycosylation / protein phosphatase inhibitor activity / manganese ion binding / Maturation of spike protein / positive regulation of cell migration ...alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase / alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity / N-Glycan antennae elongation / positive regulation of receptor signaling pathway via STAT / : / protein N-linked glycosylation / protein phosphatase inhibitor activity / manganese ion binding / Maturation of spike protein / positive regulation of cell migration / viral protein processing / Golgi membrane / Golgi apparatus / extracellular exosome / membrane
Similarity search - Function
Glycosyltransferase family 18 / Domain of unknown function DUF4525 / : / Glycosyltransferase family 18 / MGT5A-like, N-terminal
Similarity search - Domain/homology
alpha-D-mannopyranose / URIDINE-5'-DIPHOSPHATE / Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsLiu, Y. / Bineva-Todd, G. / Meek, R. / Mazo, L. / Piniello, B. / Moroz, O.V. / Begum, N. / Roustan, C. / Tomita, S. / Kjaer, S. ...Liu, Y. / Bineva-Todd, G. / Meek, R. / Mazo, L. / Piniello, B. / Moroz, O.V. / Begum, N. / Roustan, C. / Tomita, S. / Kjaer, S. / Rovira, C. / Davies, G.J. / Schumann, B.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)951231European Union
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: A Bioorthogonal Precision Tool for Human N -Acetylglucosaminyltransferase V.
Authors: Liu, Y. / Bineva-Todd, G. / Meek, R.W. / Mazo, L. / Piniello, B. / Moroz, O. / Burnap, S.A. / Begum, N. / Ohara, A. / Roustan, C. / Tomita, S. / Kjaer, S. / Polizzi, K. / Struwe, W.B. / ...Authors: Liu, Y. / Bineva-Todd, G. / Meek, R.W. / Mazo, L. / Piniello, B. / Moroz, O. / Burnap, S.A. / Begum, N. / Ohara, A. / Roustan, C. / Tomita, S. / Kjaer, S. / Polizzi, K. / Struwe, W.B. / Rovira, C. / Davies, G.J. / Schumann, B.
History
DepositionApr 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _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: Secreted alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
B: Secreted alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,4219
Polymers117,7142
Non-polymers1,7077
Water4,900272
1
A: Secreted alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8425
Polymers58,8571
Non-polymers9864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Secreted alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5784
Polymers58,8571
Non-polymers7213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.507, 69.069, 90.993
Angle α, β, γ (deg.)108.208, 92.088, 106.747
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 214 - 728 / Label seq-ID: 1 - 515

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Secreted alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A / Secreted beta-1 / 6-N-acetylglucosaminyltransferase V / Secreted GNT-V


Mass: 58856.812 Da / Num. of mol.: 2 / Mutation: F445V,F504L,E297A
Source method: isolated from a genetically manipulated source
Details: MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, and F445V, F504L bump-and-hole mutations and E297A ...Details: MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, and F445V, F504L bump-and-hole mutations and E297A mutation in the active site,MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, and F445V, F504L bump-and-hole mutations and E297A mutation in the active site
Source: (gene. exp.) Homo sapiens (human) / Gene: MGAT5, GGNT5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q09328

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Sugars , 2 types, 4 molecules

#3: 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.: 2 / 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
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 275 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15-20% PEG3350, 0.1M Tris-HCl pH 8-8.5, 0.3M Li2SO4, 0-10% ethylene glycol, Microseed matrix screening
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.72738 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72738 Å / Relative weight: 1
ReflectionResolution: 1.97→44.1 Å / Num. obs: 68392 / % possible obs: 94.4 % / Redundancy: 3.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.116 / Rrim(I) all: 0.164 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.23-44.13.60.0196900.9980.0190.027
1.97-2.013.81.55744320.271.5542.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
REFMAC5.8.0425refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→44.1 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 15.1 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2418 3266 4.782 %
Rwork0.1996 65034 -
all0.202 --
obs-68300 94.644 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.744 Å2
Baniso -1Baniso -2Baniso -3
1-0.475 Å2-0.48 Å2-1.014 Å2
2--0.507 Å20.172 Å2
3----0.494 Å2
Refinement stepCycle: LAST / Resolution: 1.97→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8018 0 106 272 8396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0128329
X-RAY DIFFRACTIONr_bond_other_d0.0020.0167727
X-RAY DIFFRACTIONr_angle_refined_deg2.1391.82711294
X-RAY DIFFRACTIONr_angle_other_deg0.7461.75617865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35151001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.407537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72101403
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.25510378
X-RAY DIFFRACTIONr_chiral_restr0.1060.21241
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029634
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021906
X-RAY DIFFRACTIONr_nbd_refined0.2260.21696
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.27129
X-RAY DIFFRACTIONr_nbtor_refined0.1780.23953
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.24404
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3150.2312
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.080.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.211
X-RAY DIFFRACTIONr_nbd_other0.1710.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2520.211
X-RAY DIFFRACTIONr_mcbond_it2.4581.9694025
X-RAY DIFFRACTIONr_mcbond_other2.4581.9694025
X-RAY DIFFRACTIONr_mcangle_it3.7963.5325019
X-RAY DIFFRACTIONr_mcangle_other3.7953.5325020
X-RAY DIFFRACTIONr_scbond_it2.7482.1814304
X-RAY DIFFRACTIONr_scbond_other2.7322.1784301
X-RAY DIFFRACTIONr_scangle_it4.2193.9126275
X-RAY DIFFRACTIONr_scangle_other4.1963.9056270
X-RAY DIFFRACTIONr_lrange_it6.43519.8619105
X-RAY DIFFRACTIONr_lrange_other6.42419.8359079
X-RAY DIFFRACTIONr_ncsr_local_group_10.1080.0515681
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.108290.05008
12AX-RAY DIFFRACTIONLocal ncs0.108290.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.0210.3532180.3474871X-RAY DIFFRACTION95.0504
2.021-2.0760.3392290.334728X-RAY DIFFRACTION95.9543
2.076-2.1360.3382350.3044577X-RAY DIFFRACTION95.3249
2.136-2.2020.3022450.2844416X-RAY DIFFRACTION95.0642
2.202-2.2740.3072130.2774276X-RAY DIFFRACTION94.8046
2.274-2.3540.2652000.2494139X-RAY DIFFRACTION94.1215
2.354-2.4420.2882360.2353927X-RAY DIFFRACTION93.2154
2.442-2.5420.2881700.2243691X-RAY DIFFRACTION90.9541
2.542-2.6540.2711550.2123434X-RAY DIFFRACTION86.8797
2.654-2.7830.2821410.2152856X-RAY DIFFRACTION77.3419
2.783-2.9330.2581750.2053431X-RAY DIFFRACTION96.4945
2.933-3.110.2521630.1893325X-RAY DIFFRACTION99.1191
3.11-3.3240.2341600.1843156X-RAY DIFFRACTION99.222
3.324-3.5880.2181530.1882913X-RAY DIFFRACTION99.3519
3.588-3.9280.2131600.162638X-RAY DIFFRACTION99.3961
3.928-4.3880.1961150.1392420X-RAY DIFFRACTION99.4508
4.388-5.0580.1631180.1242158X-RAY DIFFRACTION99.6934
5.058-6.1740.219710.1641836X-RAY DIFFRACTION99.4265
6.174-8.6480.219570.1721433X-RAY DIFFRACTION99.7991
8.648-44.10.183490.176797X-RAY DIFFRACTION99.2958
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)
10.7674-0.14010.20910.72210.18822.11040.0180.04-0.0038-0.09160.015-0.0076-0.06430.0125-0.0330.0219-0.02450.01850.17890.07090.13440.54670.9121-1.0251
20.94440.2115-0.02660.970.16131.79430.0197-0.04220.07620.0746-0.00090.026-0.0408-0.0071-0.01880.01190.00170.02280.16480.07730.12663.154439.7885-35.6928
Refinement TLS groupSelection: ALL

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