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- PDB-2ae7: Crystal Structure of Human M340H-Beta1,4-Galactosyltransferase-I ... -

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Basic information

Entry
Database: PDB / ID: 2ae7
TitleCrystal Structure of Human M340H-Beta1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Pentasaccharide
ComponentsBeta-1,4-galactosyltransferase 1
KeywordsTRANSFERASE / beta1 / 4-Galactosyltransferase-I / Pentasaccharide / Closed conformation / Mutant
Function / homology
Function and homology information


Defective B4GALT1 causes CDG-2d / galactosyltransferase activity / Interaction With Cumulus Cells And The Zona Pellucida / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / Lactose synthesis / Keratan sulfate biosynthesis / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase / N-acetyllactosamine synthase ...Defective B4GALT1 causes CDG-2d / galactosyltransferase activity / Interaction With Cumulus Cells And The Zona Pellucida / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / Lactose synthesis / Keratan sulfate biosynthesis / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase / N-acetyllactosamine synthase / N-acetyllactosamine synthase activity / positive regulation of circulating fibrinogen levels / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity / Golgi trans cisterna / N-Glycan antennae elongation / penetration of zona pellucida / UDP-galactosyltransferase activity / regulation of acrosome reaction / lactose synthase activity / lactose biosynthetic process / oligosaccharide biosynthetic process / macrophage migration / development of secondary sexual characteristics / desmosome / acute inflammatory response / galactose metabolic process / Pre-NOTCH Processing in Golgi / positive regulation of epithelial cell proliferation involved in wound healing / binding of sperm to zona pellucida / protein N-linked glycosylation / angiogenesis involved in wound healing / Transferases; Glycosyltransferases; Hexosyltransferases / azurophil granule membrane / Golgi cisterna membrane / epithelial cell development / alpha-tubulin binding / beta-tubulin binding / extracellular matrix organization / secretory granule membrane / epithelial cell proliferation / filopodium / brush border membrane / lipid metabolic process / negative regulation of epithelial cell proliferation / manganese ion binding / basolateral plasma membrane / cell adhesion / positive regulation of apoptotic process / Golgi membrane / external side of plasma membrane / Neutrophil degranulation / Golgi apparatus / protein-containing complex / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
Beta-1,4-galactosyltransferase / Galactosyltransferase, N-terminal / N-terminal region of glycosyl transferase group 7 / Galactosyltransferase, C-terminal / N-terminal domain of galactosyltransferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / : / 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE / Beta-1,4-galactosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRamasamy, V. / Ramakrishnan, B. / Boeggeman, E. / Ratner, D.M. / Seeberger, P.H. / Qasba, P.K.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Oligosaccharide Preferences of beta1,4-Galactosyltransferase-I: Crystal Structures of Met340His Mutant of Human beta1,4-Galactosyltransferase-I with a Pentasaccharide and Trisaccharides of the N-Glycan Moiety
Authors: Ramasamy, V. / Ramakrishnan, B. / Boeggeman, E. / Ratner, D.M. / Seeberger, P.H. / Qasba, P.K.
History
DepositionJul 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,4-galactosyltransferase 1
B: Beta-1,4-galactosyltransferase 1
C: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,38434
Polymers98,3203
Non-polymers5,06531
Water8,485471
1
A: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1919
Polymers32,7731
Non-polymers1,4188
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,91415
Polymers32,7731
Non-polymers2,14114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,27910
Polymers32,7731
Non-polymers1,5069
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
A: Beta-1,4-galactosyltransferase 1
hetero molecules

B: Beta-1,4-galactosyltransferase 1
C: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,38434
Polymers98,3203
Non-polymers5,06531
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
identity operation1_555x,y,z1
Buried area13880 Å2
ΔGint-239 kcal/mol
Surface area32420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.982, 195.172, 143.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Beta-1,4-galactosyltransferase 1 / E.C.2.4.1.90 / Beta-1 / 4-GalTase 1 / Beta4Gal-T1 / b4Gal-T1 / UDP-galactose:beta-N-acetylglucosamine beta-1 / 4- ...Beta-1 / 4-GalTase 1 / Beta4Gal-T1 / b4Gal-T1 / UDP-galactose:beta-N-acetylglucosamine beta-1 / 4-galactosyltransferase 1


Mass: 32773.230 Da / Num. of mol.: 3 / Fragment: Catalytic domain, Residues 126-398 / Mutation: M340H, C338T, R337T
Source method: isolated from a genetically manipulated source
Details: N-acetyllactosamine synthase part / Source: (gene. exp.) Homo sapiens (human)
Description: N-terminal carries t7 tag of 11 amino acids followed by GLY, SER & ALA
Gene: B4GALT1, GGTB2 / Plasmid: PET23A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P15291, N-acetyllactosamine synthase

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Sugars , 2 types, 3 molecules

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


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 545.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-1-2/a6-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 499 molecules

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


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-UDH / 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE


Mass: 503.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H27N3O12P2
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.8 Å3/Da / Density % sol: 67.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: mes, ammonium sulfate, dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2003 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 101444 / % possible obs: 96.5 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.094 / Net I/σ(I): 15
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 9651 / Rsym value: 0.59 / % possible all: 93.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE: 1O0R

1o0r


Resolution: 2→40 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3336750.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 9818 10 %RANDOM
Rwork0.219 ---
all0.233 97969 --
obs0.233 97969 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.3949 Å2 / ksol: 0.385291 e/Å3
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.85 Å20 Å20 Å2
2--13.61 Å20 Å2
3----9.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6636 0 306 471 7413
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 1585 9.9 %
Rwork0.284 14484 -
obs-14484 96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3udph.parudph.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION5water_rep.paramwater.top

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