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Basic information

Entry
Database: PDB / ID: 8zwp
TitleStructure-Based Mechanism and Specificity of Human Galactosyltransferase B3GalT5
ComponentsBeta-1,3-galactosyltransferase 5
KeywordsTRANSFERASE / Gb4 / globo-series biosynthesis / bi-bi mechanism / SN2-like reaction / ternary 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 / : / response to bacterium / lipid metabolic process / Golgi membrane / endoplasmic reticulum / Golgi apparatus
Similarity search - Function
Glycosyl transferase, family 31 / Galactosyltransferase
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE / Beta-1,3-galactosyltransferase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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 / Category: citation / citation_author
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

Downloads & links

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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)70,69715
Polymers65,1012
Non-polymers5,59613
Water5,332296
1
A: Beta-1,3-galactosyltransferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9957
Polymers32,5511
Non-polymers2,4446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-1,3-galactosyltransferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7028
Polymers32,5511
Non-polymers3,1527
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.646, 86.360, 87.187
Angle α, β, γ (deg.)90.000, 95.470, 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 160 or resid 162...
d_2ens_1(chain "B" and (resid 43 through 160 or resid 162...
d_1ens_2chain "E"
d_2ens_2chain "G"

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_1ASNASNPHEPHEAA43 - 16013 - 130
d_12ens_1ASNASNLYSLYSAA162 - 202132 - 172
d_13ens_1GLUGLUPHEPHEAA204 - 286174 - 256
d_14ens_1LYSLYSPROPROAA288 - 308258 - 278
d_15ens_1MNMNMNMNAI401
d_16ens_1UDPUDPUDPUDPAJ402
d_17ens_1B3PB3PB3PB3PAK403
d_18ens_1NGANGANGANGACC4
d_19ens_1GLAGLAGLAGLACC3
d_110ens_1GALGALGALGALCC2
d_111ens_1BGCBGCBGCBGCCC1
d_21ens_1ASNASNPHEPHEBB43 - 16013 - 130
d_22ens_1ASNASNLYSLYSBB162 - 202132 - 172
d_23ens_1GLUGLUPHEPHEBB204 - 286174 - 256
d_24ens_1LYSLYSPROPROBB288 - 308258 - 278
d_25ens_1MNMNMNMNBL401
d_26ens_1UDPUDPUDPUDPBM402
d_27ens_1B3PB3PB3PB3PBN403
d_28ens_1NGANGANGANGADD4
d_29ens_1GLAGLAGLAGLADD3
d_210ens_1GALGALGALGALDD2
d_211ens_1BGCBGCBGCBGCDD1
d_11ens_2NAGNAGNAGNAGEE1
d_12ens_2NAGNAGNAGNAGEE2
d_21ens_2NAGNAGNAGNAGGG1
d_22ens_2NAGNAGNAGNAGGG2

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.189324760627, 0.0117769650148, -0.981843897017), (-0.0247516598137, 0.999667572662, 0.00721799868782), (0.981602511381, 0.0229357202553, 0.189553323332)38.813959086, 8.96138791516, -27.313599814
2given(-0.399401218097, 0.767190683335, -0.501893536904), (0.666640973394, -0.132771341891, -0.733458644617), (-0.629339717143, -0.627527072066, -0.458411708238)30.8136966675, 27.0281785616, 46.559491036

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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 , 5 types, 7 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D- ...2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpNAcb1-3DGalpa1-4DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{[(3+1)][b-D-GalpNAc]{}}}}LINUCSPDB-CARE
#3: 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: obtained synthetically
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
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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
#9: 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.: 1 / 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

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Non-polymers , 4 types, 302 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
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.74 Å3/Da / Density % sol: 55.16 %
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 PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 58604 / % possible obs: 99.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 27.02 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 21.95
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 5703 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Blu-Icedata collection
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→28.93 Å / SU ML: 0.2228 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2358
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2334 2983 5.09 %
Rwork0.1987 55578 -
obs0.2005 58561 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.16 Å2
Refinement stepCycle: LAST / Resolution: 1.86→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 365 296 5043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00694879
X-RAY DIFFRACTIONf_angle_d0.94716614
X-RAY DIFFRACTIONf_chiral_restr0.0584779
X-RAY DIFFRACTIONf_plane_restr0.0102789
X-RAY DIFFRACTIONf_dihedral_angle_d15.08041846
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.770329728798
ens_2d_2EEX-RAY DIFFRACTIONTorsion NCS2.84763970855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.890.32371310.29942553X-RAY DIFFRACTION95.96
1.89-1.920.31491360.27262590X-RAY DIFFRACTION98.52
1.92-1.960.25471350.25832606X-RAY DIFFRACTION99.06
1.96-20.28921320.24392652X-RAY DIFFRACTION99.07
2-2.040.27351350.24782631X-RAY DIFFRACTION99.32
2.04-2.080.24451450.2322648X-RAY DIFFRACTION99.25
2.08-2.130.2681240.22362638X-RAY DIFFRACTION99.21
2.13-2.180.24491320.22292675X-RAY DIFFRACTION99.33
2.18-2.240.26711580.22452634X-RAY DIFFRACTION99.64
2.24-2.310.27411460.21772609X-RAY DIFFRACTION99.46
2.31-2.380.26861630.21682668X-RAY DIFFRACTION99.75
2.38-2.470.25711290.21632656X-RAY DIFFRACTION99.54
2.47-2.570.2521440.22232622X-RAY DIFFRACTION99.82
2.57-2.680.25511770.22152644X-RAY DIFFRACTION99.89
2.68-2.820.2851280.21922668X-RAY DIFFRACTION99.89
2.82-30.27661140.21912699X-RAY DIFFRACTION99.89
3-3.230.27351630.2052637X-RAY DIFFRACTION99.93
3.23-3.560.24141450.20082677X-RAY DIFFRACTION99.89
3.56-4.070.17931680.16962647X-RAY DIFFRACTION100
4.07-5.120.18381690.14652666X-RAY DIFFRACTION99.54
5.13-28.930.18861090.16492758X-RAY DIFFRACTION99.62

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