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Basic information

Entry
Database: PDB / ID: 8zwr
TitleStructure-Based Mechanism and Specificity of Human Galactosyltransferase B3GalT5
ComponentsBeta-1,3-galactosyltransferase 5
KeywordsTRANSFERASE / globo-series glycosphingolipid biosynthesis / Oxocarbenium / SN2-like / 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 / Golgi apparatus / endoplasmic reticulum
Similarity search - Function
Glycosyl transferase, family 31 / Galactosyltransferase
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUOROGALACTOSE / Beta-1,3-galactosyltransferase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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

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)69,18512
Polymers65,1012
Non-polymers4,08410
Water5,080282
1
A: Beta-1,3-galactosyltransferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2486
Polymers32,5511
Non-polymers1,6975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-1,3-galactosyltransferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9376
Polymers32,5511
Non-polymers2,3875
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.739, 85.737, 87.730
Angle α, β, γ (deg.)90.000, 95.516, 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 197 or resid 199...
d_2ens_1(chain "B" and (resid 43 through 197 or resid 199...
d_1ens_2(chain "D" and resid 1)
d_2ens_2(chain "E" and resid 1)
d_3ens_2(chain "G" and resid 1)

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 - 19713 - 167
d_12ens_1PHEPHELYSLYSAA199 - 202169 - 172
d_13ens_1GLUGLUPHEPHEAA204 - 286174 - 256
d_14ens_1LYSLYSPROPROAA288 - 308258 - 278
d_15ens_1MNMNMNMNAG401
d_16ens_1B3PB3PB3PB3PAH402
d_17ens_1UPFUPFUPFUPFAI403
d_21ens_1ASNASNLYSLYSBB43 - 19713 - 167
d_22ens_1PHEPHELYSLYSBB199 - 202169 - 172
d_23ens_1GLUGLUPHEPHEBB204 - 286174 - 256
d_24ens_1LYSLYSPROPROBB288 - 308258 - 278
d_25ens_1MNMNMNMNBJ401
d_26ens_1B3PB3PB3PB3PBK402
d_27ens_1UPFUPFUPFUPFBL403
d_11ens_2NAGNAGNAGNAGDF1
d_21ens_2NAGNAGNAGNAGEC1
d_31ens_2NAGNAGNAGNAGGD1

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.188627482699, 0.0038065744888, -0.982041334548), (-0.0205211727125, 0.999789416366, -6.6274465223E-5), (0.981834280437, 0.0201651410226, 0.188665876211)39.0244069211, 9.10777064913, -27.3406475158
2given(0.4311469709, -0.541320298133, 0.72186191499), (-0.393874676768, -0.832702953139, -0.389189582125), (0.811772768996, -0.116525218999, -0.572229713361)-6.26378627731, 33.9995152255, 65.2384169754
3given(-0.773628252412, -0.0333942070165, 0.632759159561), (-0.323572001714, -0.837769768357, -0.439821526227), (0.544793985628, -0.54500150657, 0.637316931408)-22.8773653979, 45.7553949696, -23.1886626805

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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
Details: The recombinant protein used for crystallization contains the luminal domain of residues F31-P308, but only residues K40-P308 are well defined in the electron density maps.
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 , 3 types, 4 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: 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
#3: 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
#4: 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)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 288 molecules

#5: 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
#6: 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
#7: Chemical ChemComp-UPF / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUOROGALACTOSE / URIDINE-5'-MONOPHOSPHATE 2-DEOXY-2-FLUORO-GALACTOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 568.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23FN2O16P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.75 Å3/Da / Density % sol: 55.19 %
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: Aug 27, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 43714 / % possible obs: 94.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.61 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.93
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 2664 / % possible all: 74.3

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Blu-Icedata collection
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→30.71 Å / SU ML: 0.1907 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.7875
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.216 2114 4.84 %
Rwork0.1926 41600 -
obs0.1937 43714 83.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.79 Å2
Refinement stepCycle: LAST / Resolution: 1.94→30.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 263 282 4927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00874787
X-RAY DIFFRACTIONf_angle_d1.16046492
X-RAY DIFFRACTIONf_chiral_restr0.0817738
X-RAY DIFFRACTIONf_plane_restr0.0273786
X-RAY DIFFRACTIONf_dihedral_angle_d16.29511830
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.726436417299
ens_2d_2FDX-RAY DIFFRACTIONTorsion NCS0.96023485516
ens_2d_3FDX-RAY DIFFRACTIONTorsion NCS0.974577384631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.980.2552380.2355978X-RAY DIFFRACTION29.17
1.99-2.030.2432710.24761417X-RAY DIFFRACTION42.83
2.03-2.090.2413940.24141854X-RAY DIFFRACTION55.96
2.09-2.150.27561140.22272147X-RAY DIFFRACTION66.81
2.15-2.220.24711380.22422589X-RAY DIFFRACTION78.57
2.22-2.30.26431390.2172924X-RAY DIFFRACTION88.12
2.3-2.390.23651770.22023224X-RAY DIFFRACTION97.59
2.39-2.50.25681680.22083276X-RAY DIFFRACTION99.65
2.5-2.630.24091850.21673277X-RAY DIFFRACTION99.88
2.63-2.80.22982170.20883266X-RAY DIFFRACTION99.94
2.8-3.010.28071630.21183284X-RAY DIFFRACTION99.97
3.01-3.320.22621300.20113345X-RAY DIFFRACTION99.86
3.32-3.80.19981700.18073310X-RAY DIFFRACTION99.63
3.8-4.780.15731590.14723339X-RAY DIFFRACTION99.49
4.78-30.710.16551510.16013370X-RAY DIFFRACTION99.35
Refinement TLS params.Method: refined / Origin x: 8.80017421636 Å / Origin y: 7.99195361958 Å / Origin z: 15.1085792878 Å
111213212223313233
T0.293863224247 Å2-0.0425868542015 Å2-0.0152686820749 Å2-0.183984711725 Å20.0106843202531 Å2--0.184474886527 Å2
L0.358079794849 °2-0.0946089116711 °20.578319141957 °2-0.241307727488 °20.101967277552 °2--1.01836013062 °2
S-0.0579904251034 Å °0.14863745743 Å °0.0269807818584 Å °-0.292114469727 Å °0.0131921815287 Å °0.0702212759151 Å °-0.143445976032 Å °0.158335041653 Å °0.0403723716842 Å °
Refinement TLS groupSelection details: all

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