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- PDB-8zx9: Structure-Based Mechanism and Specificity of Human Galactosyltran... -

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Basic information

Entry
Database: PDB / ID: 8zx9
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
beta-D-galactopyranose / : / DI(HYDROXYETHYL)ETHER / URIDINE-5'-DIPHOSPHATE / Beta-1,3-galactosyltransferase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 14, 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)69,53617
Polymers65,1012
Non-polymers4,43515
Water3,963220
1
A: Beta-1,3-galactosyltransferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,58210
Polymers32,5511
Non-polymers2,0329
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-1,3-galactosyltransferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9547
Polymers32,5511
Non-polymers2,4036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.980, 86.337, 87.509
Angle α, β, γ (deg.)90.000, 95.480, 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 42 through 313)
d_2ens_1chain "B"
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_1GLYGLYPROPROAA42 - 30812 - 278
d_12ens_1MNMNMNMNAG401
d_13ens_1UDPUDPUDPUDPAH402
d_14ens_1GALGALGALGALAI403
d_15ens_1B3PB3PB3PB3PAJ404
d_21ens_1GLYGLYPROPROBB42 - 30812 - 278
d_22ens_1MNMNMNMNBN401
d_23ens_1UDPUDPUDPUDPBO402
d_24ens_1GALGALGALGALBP403
d_25ens_1B3PB3PB3PB3PBQ404
d_11ens_2NAGNAGNAGNAGDE1
d_21ens_2NAGNAGNAGNAGEC1
d_31ens_2NAGNAGNAGNAGGF1

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.184025554014, 0.000815610260217, -0.982921121072), (-0.020268031944, 0.99979018571, -0.00296503616746), (0.982712471861, 0.0204675191037, 0.184003473638)39.0627565496, 9.26063246109, -27.3095076255
2given(0.365089452999, -0.388006423307, 0.846262788253), (-0.381573437467, -0.891514619148, -0.244138066811), (0.849182785464, -0.233779167846, -0.473535529346)-13.4887709411, 26.343023619, 60.2365733255
3given(-0.840033403414, 0.119990409374, 0.529099407301), (-0.304859150833, -0.911106289191, -0.277391831078), (0.448781438232, -0.394319199956, 0.801939891291)-18.2123155009, 37.5274294499, -32.7847843371

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-1,3-galactosyltransferase 5


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

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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: 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
#7: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 229 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-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.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
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: Jan 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 36358 / % possible obs: 98.3 % / Redundancy: 4.4 % / Biso Wilson estimate: 30.89 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.12
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.551 / Num. unique obs: 1682 / % possible all: 89

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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: 2.3→26.63 Å / SU ML: 0.2668 / Cross valid method: FREE R-VALUE / Phase error: 23.4405
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2123 1504 5.24 %
Rwork0.1805 27191 -
obs0.1821 28688 90.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.63 Å2
Refinement stepCycle: LAST / Resolution: 2.3→26.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 284 220 4890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00954783
X-RAY DIFFRACTIONf_angle_d1.35386467
X-RAY DIFFRACTIONf_chiral_restr0.0765732
X-RAY DIFFRACTIONf_plane_restr0.0329783
X-RAY DIFFRACTIONf_dihedral_angle_d16.48321817
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.710721087689
ens_2d_2EDX-RAY DIFFRACTIONTorsion NCS0.29856932576
ens_2d_3EDX-RAY DIFFRACTIONTorsion NCS0.288028475029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.2846910.23771682X-RAY DIFFRACTION53.79
2.37-2.460.2674960.22861840X-RAY DIFFRACTION67.62
2.46-2.560.24021100.22832265X-RAY DIFFRACTION82.55
2.56-2.670.26731230.22392615X-RAY DIFFRACTION95.04
2.67-2.810.29341280.22582723X-RAY DIFFRACTION99.3
2.81-2.990.24491630.21132705X-RAY DIFFRACTION99.62
2.99-3.220.26731520.20022705X-RAY DIFFRACTION99.83
3.22-3.540.23271290.19132726X-RAY DIFFRACTION99.79
3.54-4.050.19781350.14962741X-RAY DIFFRACTION99.93
4.06-5.10.15291850.13542715X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 8.73585193266 Å / Origin y: 8.13495167893 Å / Origin z: 14.8621688106 Å
111213212223313233
T0.289179870139 Å2-0.0333151532233 Å20.00175128917557 Å2-0.215822369893 Å20.00754835517244 Å2--0.23255145422 Å2
L0.389614363078 °2-0.208490827511 °20.577024374157 °2-0.0947656379215 °2-0.102589504178 °2--1.15585323711 °2
S-0.0274984749549 Å °0.140196992321 Å °0.0239613226136 Å °-0.203232270211 Å °-0.0251568525633 Å °0.0361456396547 Å °-0.0603463529494 Å °0.166555413882 Å °0.0542071327263 Å °
Refinement TLS groupSelection details: all

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