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- PDB-8zx3: Structure-Based Mechanism and Specificity of Human Galactosyltran... -

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Basic information

Entry
Database: PDB / ID: 8zx3
TitleStructure-Based Mechanism and Specificity of Human Galactosyltransferase B3GalT5
ComponentsBeta-1,3-galactosyltransferase 5
KeywordsTRANSFERASE / globo-series glycosphingolipid biosynthesis / Oxocarbenium / SNi-like / SN2-like / double displacement / inverting galactosyltransferase / Michaelis complex
Function / homology
Function and homology information


Lewis blood group biosynthesis / N-acetyl-beta-D-glucosaminide beta-(1,3)-galactosyltransferase activity / oligosaccharide biosynthetic process / protein O-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / protein glycosylation / response to bacterium / lipid metabolic process / Golgi membrane / endoplasmic reticulum / Golgi apparatus
Similarity search - Function
Glycosyl transferase, family 31 / Galactosyltransferase
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / THREONINE / URIDINE-5'-DIPHOSPHATE / Beta-1,3-galactosyltransferase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsLo, J.M. / Ma, C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Structure-Based Mechanism and Specificity of Human Galactosyltransferase beta 3GalT5.
Authors: Lo, J.M. / Kung, C.C. / Cheng, T.R. / Wong, C.H. / Ma, C.
History
DepositionJun 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-1,3-galactosyltransferase 5
B: Beta-1,3-galactosyltransferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,15618
Polymers65,1012
Non-polymers5,05516
Water5,314295
1
A: Beta-1,3-galactosyltransferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,83910
Polymers32,5511
Non-polymers2,2899
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-1,3-galactosyltransferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3178
Polymers32,5511
Non-polymers2,7667
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.544, 86.367, 86.888
Angle α, β, γ (deg.)90.000, 95.260, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 43 through 202 or resid 204 through 286 or resid 288 through 312))
d_2ens_1(chain "B" and (resid 43 through 202 or resid 204 through 286 or resid 288 through 312))
d_1ens_2(chain "E" and resid 1)
d_2ens_2(chain "F" and resid 1)
d_3ens_2(chain "G" and resid 1)
d_1ens_3chain "I"
d_2ens_3chain "J"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ASNASNLYSLYSAA43 - 20213 - 172
d_12ens_1GLUGLUPHEPHEAA204 - 286174 - 256
d_13ens_1LYSLYSPROPROAA288 - 308258 - 278
d_14ens_1MNMNMNMNAI401
d_15ens_1UDPUDPUDPUDPAJ402
d_16ens_1B3PB3PB3PB3PAK403
d_21ens_1ASNASNLYSLYSBB43 - 20213 - 172
d_22ens_1GLUGLUPHEPHEBB204 - 286174 - 256
d_23ens_1LYSLYSPROPROBB288 - 308258 - 278
d_24ens_1MNMNMNMNBO401
d_25ens_1UDPUDPUDPUDPBP402
d_26ens_1B3PB3PB3PB3PBQ403
d_11ens_2NAGNAGNAGNAGEC1
d_21ens_2NAGNAGNAGNAGFD1
d_31ens_2NAGNAGNAGNAGGE1
d_11ens_3NAGNAGNAGNAGIG2
d_12ens_3NGANGANGANGAIG1
d_13ens_3THRTHRTHRTHRAN406
d_21ens_3NAGNAGNAGNAGJH2
d_22ens_3NGANGANGANGAJH1
d_23ens_3THRTHRTHRTHRBR404

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.195837252568, 0.00840757033429, -0.980600368788), (-0.0276347605064, 0.999613429142, 0.00305160464437), (0.980246953843, 0.0265010384744, 0.195993888786)38.3752220546, 9.36370688268, -27.554628869
2given(0.345847410911, -0.38785664324, 0.854375088975), (-0.381669771711, -0.889981340455, -0.249522341694), (0.8571567848, -0.239792489325, -0.455830898838)-35.41636297, 32.5757193767, 45.1603041726
3given(0.166326584074, 0.0286020493298, -0.985655817314), (0.0253288402259, 0.999125493064, 0.0332670852611), (0.985745361279, -0.030498719368, 0.165456673585)39.3039374497, 6.86066000814, -25.8892195908
4given(0.227970058131, 0.107818313715, -0.967680145411), (-0.120033191395, 0.989381053701, 0.0819583036683), (0.966241008009, 0.097469696852, 0.238491032612)36.8822626668, 8.22138929699, -29.1668979331

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-1,3-galactosyltransferase 5 / Beta-1 / 3-GalTase 5 / Beta3Gal-T5 / Beta3GalT5 / b3Gal-T5 / Beta-3-Gx-T5 / UDP-Gal:beta-GlcNAc ...Beta-1 / 3-GalTase 5 / Beta3Gal-T5 / Beta3GalT5 / b3Gal-T5 / Beta-3-Gx-T5 / UDP-Gal:beta-GlcNAc beta-1 / 3-galactosyltransferase 5 / UDP-galactose:beta-N-acetylglucosamine beta-1


Mass: 32550.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B3GALT5 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y2C3, Transferases; Glycosyltransferases; Hexosyltransferases

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Sugars , 4 types, 6 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: 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: obtained synthetically
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(6+1)][b-L-Fucp]{}}LINUCSPDB-CARE
#4: 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-3DGalpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc]{[(3+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 6 types, 305 molecules

#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#8: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M BIS-TRIS Propane pH8.5, 0.2M Potassium Sodium Tartrate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 39469 / % possible obs: 94.1 % / Redundancy: 4 % / Biso Wilson estimate: 19.29 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 28.02
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 3113 / % possible all: 73.9

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Blu-Icedata collection
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→26.47 Å / SU ML: 0.2086 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.8236
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2288 2050 5.19 %
Rwork0.2016 37419 -
obs0.203 39469 95.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.64 Å2
Refinement stepCycle: LAST / Resolution: 2.09→26.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 327 295 5004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01264831
X-RAY DIFFRACTIONf_angle_d1.6746538
X-RAY DIFFRACTIONf_chiral_restr0.1855749
X-RAY DIFFRACTIONf_plane_restr0.0461790
X-RAY DIFFRACTIONf_dihedral_angle_d18.15381830
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.973516848642
ens_2d_2CEX-RAY DIFFRACTIONTorsion NCS0.23390019465
ens_2d_3CEX-RAY DIFFRACTIONTorsion NCS0.171588205724
ens_3d_2GIX-RAY DIFFRACTIONTorsion NCS1.15813877163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.2794910.23251945X-RAY DIFFRACTION73.61
2.14-2.190.25681090.22792090X-RAY DIFFRACTION79.96
2.19-2.250.27781380.23222233X-RAY DIFFRACTION86.03
2.25-2.320.25531410.23082368X-RAY DIFFRACTION91.74
2.32-2.390.26581460.22562550X-RAY DIFFRACTION97.29
2.39-2.480.25561260.23722591X-RAY DIFFRACTION99.63
2.48-2.580.26471600.23482606X-RAY DIFFRACTION100
2.58-2.690.26881540.21952593X-RAY DIFFRACTION100
2.69-2.840.2411240.2262634X-RAY DIFFRACTION100
2.84-3.010.26621170.22312649X-RAY DIFFRACTION100
3.01-3.250.24981610.1992595X-RAY DIFFRACTION100
3.25-3.570.22771420.20242632X-RAY DIFFRACTION99.96
3.57-4.090.18821730.16822620X-RAY DIFFRACTION100
4.09-5.140.18191670.15832620X-RAY DIFFRACTION100
5.14-26.470.19161010.18312693X-RAY DIFFRACTION98.83
Refinement TLS params.Method: refined / Origin x: 8.70450689758 Å / Origin y: 8.00755530282 Å / Origin z: 15.1951545893 Å
111213212223313233
T0.354779022722 Å2-0.0662577892482 Å2-0.0108902283869 Å2-0.197013386992 Å20.0260659315736 Å2--0.185289055267 Å2
L0.321700007994 °2-0.204959393739 °20.627942233833 °2-0.28222249516 °20.055929990965 °2--0.943512316004 °2
S-0.0646293142284 Å °0.198883216122 Å °-0.00463447120136 Å °-0.392315488966 Å °0.0456646186943 Å °0.0650996625295 Å °-0.124673823663 Å °0.166554145108 Å °0.0255979803024 Å °
Refinement TLS groupSelection details: all

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