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- PDB-12em: Crystal structure of a B1,3-Glucosyltransferase (B3GLCT) reveals ... -

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Basic information

Entry
Database: PDB / ID: 12em
TitleCrystal structure of a B1,3-Glucosyltransferase (B3GLCT) reveals an unusual mode of substrate recognition by a two-domain GT-A fold glycosyltransferase
Components
  • Beta-1,3-glucosyltransferase
  • Thrombospondin-1
KeywordsCARBOHYDRATE / O-fucosylation / Glycosyltransferase / Peters Plus Syndrome / Thrombospondin Type 1 Repeats
Function / homology
Function and homology information


O-fucosylpeptide 3-beta-glucosyltransferase activity / negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / negative regulation of nitric oxide-cGMP mediated signal transduction / collagen V binding / thrombospondin complex / negative regulation of dendritic cell antigen processing and presentation / : / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / protein O-linked glycosylation via fucose / negative regulation of sprouting angiogenesis ...O-fucosylpeptide 3-beta-glucosyltransferase activity / negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / negative regulation of nitric oxide-cGMP mediated signal transduction / collagen V binding / thrombospondin complex / negative regulation of dendritic cell antigen processing and presentation / : / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / protein O-linked glycosylation via fucose / negative regulation of sprouting angiogenesis / chronic inflammatory response / negative regulation of endothelial cell chemotaxis / Defective B3GALTL causes PpS / negative regulation of fibroblast growth factor receptor signaling pathway / O-glycosylation of TSR domain-containing proteins / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of long-chain fatty acid import across plasma membrane / positive regulation of transforming growth factor beta1 production / acetylglucosaminyltransferase activity / fucose metabolic process / fibrinogen complex / negative regulation of interleukin-12 production / blood coagulation, fibrin clot formation / engulfment of apoptotic cell / low-density lipoprotein particle binding / negative regulation of focal adhesion assembly / Signaling by PDGF / platelet alpha granule / negative regulation of plasminogen activation / positive regulation of chemotaxis / fibrinogen binding / negative regulation of cell migration involved in sprouting angiogenesis / positive regulation of macrophage activation / sprouting angiogenesis / transforming growth factor beta binding / positive regulation of fibroblast migration / proteoglycan binding / negative regulation of cell-matrix adhesion / negative regulation of endothelial cell migration / negative regulation of receptor guanylyl cyclase signaling pathway / Transferases; Glycosyltransferases; Hexosyltransferases / negative regulation of interleukin-10 production / Syndecan interactions / extracellular matrix structural constituent / response to testosterone / phosphatidylserine binding / negative regulation of endothelial cell proliferation / endopeptidase inhibitor activity / glycosyltransferase activity / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of macrophage chemotaxis / behavioral response to pain / response to progesterone / fibronectin binding / negative regulation of blood vessel endothelial cell migration / fibroblast growth factor binding / negative regulation of fibrinolysis / positive regulation of phosphorylation / negative regulation of tumor necrosis factor production / response to glucose / positive regulation of endothelial cell apoptotic process / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / response to magnesium ion / Integrin cell surface interactions / response to mechanical stimulus / nitric oxide-cGMP-mediated signaling / negative regulation of angiogenesis / laminin binding / positive regulation of smooth muscle cell proliferation / positive regulation of endothelial cell migration / secretory granule / platelet alpha granule lumen / response to endoplasmic reticulum stress / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of translation / sarcoplasmic reticulum / cellular response to tumor necrosis factor / response to calcium ion / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cellular response to growth factor stimulus / integrin binding / positive regulation of reactive oxygen species metabolic process / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / Platelet degranulation / cell migration / heparin binding / cellular response to heat / protease binding / extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to hypoxia / positive regulation of MAPK cascade / cell adhesion / response to xenobiotic stimulus / immune response / positive regulation of cell migration / inflammatory response / negative regulation of cell population proliferation
Similarity search - Function
Fringe-like / Fringe-like / Thrombospondin, C-terminal / Thrombospondin, type 3 repeat / Thrombospondin C-terminal region / Thrombospondin type-3 (TSP3) repeat profile. / Thrombospondin C-terminal domain profile. / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat ...Fringe-like / Fringe-like / Thrombospondin, C-terminal / Thrombospondin, type 3 repeat / Thrombospondin C-terminal region / Thrombospondin type-3 (TSP3) repeat profile. / Thrombospondin C-terminal domain profile. / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat / : / Thrombospondin N-terminal -like domains. / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Thrombospondin type 1 domain / Endoplasmic reticulum targeting sequence. / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Nucleotide-diphospho-sugar transferases / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
alpha-L-fucopyranose / : / URIDINE-5'-DIPHOSPHATE / Thrombospondin-1 / Beta-1,3-glucosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsBerardinelli, S.J. / Kadirvelraj, R. / Wood, Z.A.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM148433 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01HD096030 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM130915 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103390 United States
National Science Foundation (NSF, United States)2400220 United States
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Crystal structure of a beta 1,3-Glucosyltransferase reveals an unusual substrate recognition by a two-domain GT-A fold glycosyltransferase.
Authors: Berardinelli, S.J. / Kadirvelraj, R. / Luther, K.B. / Gao, Z. / Chapla, D. / Huang, C. / Tehrani, D.M. / Zhang, A. / Moremen, K.W. / Wood, Z.A. / Haltiwanger, R.S.
History
DepositionMar 30, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,3-glucosyltransferase
B: Thrombospondin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9388
Polymers55,9402
Non-polymers9996
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-16 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.910, 133.910, 137.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Beta-1,3-glucosyltransferase / Beta3Glc-T / Beta 3-glucosyltransferase / Beta-3-glycosyltransferase-like


Mass: 49371.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Glycosyltransferase / Source: (gene. exp.) Homo sapiens (human) / Gene: B3GLCT, B3GALTL, B3GTL / Cell line (production host): HEK293-F cells / Production host: Homo sapiens (human)
References: UniProt: Q6Y288, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Protein Thrombospondin-1 / Glycoprotein G


Mass: 6568.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THBS1, TSP, TSP1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P07996

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Sugars , 2 types, 2 molecules

#5: 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
#8: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 116 molecules

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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.22 Å3/Da / Density % sol: 61.84 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 34% PEG 3350, 0.2 M dibasic ammonium phosphate and 0.5 M betaine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2021
RadiationMonochromator: Si (111) Rosenbaum-Rock double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→57.98 Å / Num. obs: 45560 / % possible obs: 99.8 % / Redundancy: 18.2 % / CC1/2: 0.999 / Net I/σ(I): 21.1
Reflection shellResolution: 2.06→2.18 Å / Num. unique obs: 7200 / CC1/2: 0.548 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→57.98 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 2243 5 %
Rwork0.1992 --
obs0.2006 44862 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→57.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3899 0 60 112 4071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124074
X-RAY DIFFRACTIONf_angle_d1.0915537
X-RAY DIFFRACTIONf_dihedral_angle_d14.5271496
X-RAY DIFFRACTIONf_chiral_restr0.06603
X-RAY DIFFRACTIONf_plane_restr0.01698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.110.36541370.31662604X-RAY DIFFRACTION100
2.12-2.160.34171370.29972610X-RAY DIFFRACTION100
2.16-2.220.28131380.25452605X-RAY DIFFRACTION100
2.22-2.280.27071390.24912637X-RAY DIFFRACTION100
2.28-2.350.25891390.2322640X-RAY DIFFRACTION100
2.35-2.420.31071360.23912595X-RAY DIFFRACTION100
2.42-2.510.29511390.23972642X-RAY DIFFRACTION100
2.51-2.610.24191380.21172634X-RAY DIFFRACTION100
2.61-2.730.25771400.19862644X-RAY DIFFRACTION100
2.73-2.870.24321400.20582652X-RAY DIFFRACTION100
2.87-3.050.26371400.21472659X-RAY DIFFRACTION100
3.05-3.290.30391400.22732662X-RAY DIFFRACTION100
3.29-3.620.22951420.19592690X-RAY DIFFRACTION100
3.62-4.140.19421410.18262687X-RAY DIFFRACTION100
4.14-5.210.16051450.15842749X-RAY DIFFRACTION100
5.22-57.980.22791520.20242909X-RAY DIFFRACTION100
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)
11.1612-0.73520.50652.55760.4233.24040.1590.0996-0.1602-0.09690.01120.06550.54510.369100.52080.036-0.10150.52660.00270.543810.8736.7598-19.3757
21.1284-0.34050.18121.4550.61944.7189-0.0098-0.31320.06480.28980.07480.01420.1489-0.37140.00010.5048-0.0199-0.04510.59640.05250.5987-1.451748.32720.9906
30.0409-0.0230.03030.0138-0.01530.0248-0.29950.01970.1074-0.2238-0.15430.1171-0.1673-0.3111-0.00020.94780.29420.02411.00640.10830.6547-17.393781.5931-34.3914
40.24930.2378-0.18780.4289-0.08940.17990.08410.1052-0.29960.08520.15310.042-0.23-0.1614-00.64660.0204-0.00860.59830.01560.7108-4.959569.9583-15.0731
50.0856-0.02560.00370.0085-0.00450.0122-0.0092-0.0472-0.02720.1301-0.00210.67480.0645-0.4814-0.00010.5847-0.09660.02271.137-0.14560.7607-19.223576.9117-34.7103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 205 )
2X-RAY DIFFRACTION2chain 'A' and (resid 206 through 480 )
3X-RAY DIFFRACTION3chain 'B' and (resid 8 through 12 )
4X-RAY DIFFRACTION4chain 'B' and (resid 13 through 42 )
5X-RAY DIFFRACTION5chain 'B' and (resid 43 through 47 )

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