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- PDB-2fyc: Crystal structure of the catalytic domain of bovine beta1,4-galac... -

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Basic information

Entry
Database: PDB / ID: 2fyc
TitleCrystal structure of the catalytic domain of bovine beta1,4-galactosyltransferase-I in complex with alpha-lactalbumin, Ca and UDP-galactose
Components
  • Alpha-lactalbumin
  • beta-1,4-galactosyltransferase
KeywordsTRANSFERASE / lactose synthase / M344H mutation / Ca binding
Function / homology
Function and homology information


Lactose synthesis / protein galactosylation / Keratan sulfate biosynthesis / Interaction With Cumulus Cells And The Zona Pellucida / Lactose synthesis / N-Glycan antennae elongation / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase / N-acetyllactosamine synthase ...Lactose synthesis / protein galactosylation / Keratan sulfate biosynthesis / Interaction With Cumulus Cells And The Zona Pellucida / Lactose synthesis / N-Glycan antennae elongation / 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 / UDP-galactosyltransferase activity / Golgi trans cisterna / lactose synthase activity / lactose biosynthetic process / oligosaccharide biosynthetic process / desmosome / protein N-linked glycosylation / Neutrophil degranulation / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / beta-tubulin binding / alpha-tubulin binding / cytoskeletal protein binding / filopodium / brush border membrane / lipid metabolic process / lysozyme activity / manganese ion binding / basolateral plasma membrane / external side of plasma membrane / calcium ion binding / Golgi apparatus / protein-containing complex / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Lactalbumin / 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 / Lysozyme - #10 ...Lactalbumin / 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 / Lysozyme - #10 / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GALACTOSE-URIDINE-5'-DIPHOSPHATE / URIDINE-5'-DIPHOSPHATE / Beta-1,4-galactosyltransferase 1 / Alpha-lactalbumin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRamakrishnan, B. / Ramasamy, V. / Qasba, P.K.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Snapshots of beta-1,4-Galactosyltransferase-I Along the Kinetic Pathway.
Authors: Ramakrishnan, B. / Ramasamy, V. / Qasba, P.K.
History
DepositionFeb 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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 / _struct_conn.pdbx_dist_value / _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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 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: Alpha-lactalbumin
B: beta-1,4-galactosyltransferase
C: Alpha-lactalbumin
D: beta-1,4-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,04113
Polymers93,7454
Non-polymers2,2969
Water13,781765
1
A: Alpha-lactalbumin
B: beta-1,4-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1187
Polymers46,8722
Non-polymers1,2465
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Alpha-lactalbumin
D: beta-1,4-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9236
Polymers46,8722
Non-polymers1,0514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.374, 94.615, 99.603
Angle α, β, γ (deg.)90.00, 101.78, 90.00
Int Tables number4
Space group name H-MP1211
Details1:1 complex between the alpha-lactalbumin and the catalytic domain of beta 1, 4-galactosyltransferase

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Alpha-lactalbumin / Lactose synthase B protein


Mass: 14015.835 Da / Num. of mol.: 2 / Mutation: C342T, M344H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lalba / Plasmid: pEt17.1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P29752
#2: Protein beta-1,4-galactosyltransferase


Mass: 32856.531 Da / Num. of mol.: 2 / Fragment: residues 57-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pET23a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P08037, Transferases; Glycosyltransferases; Hexosyltransferases

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Non-polymers , 5 types, 774 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#6: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 765 / 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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 500 Mes-NaOH, 6% PEG 4000%, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2003 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.98→32.56 Å / Num. obs: 69858 / % possible obs: 96 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.043 / Net I/σ(I): 17
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 6450 / Rsym value: 0.465 / % possible all: 89

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OQM

1oqm


Resolution: 2→32.56 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1664884.26 / 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 6867 10.1 %RANDOM
Rwork0.2 ---
obs0.2 67737 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.4715 Å2 / ksol: 0.338919 e/Å3
Displacement parametersBiso mean: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.23 Å20 Å23.99 Å2
2--4.16 Å20 Å2
3----8.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-6 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→32.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6402 0 138 765 7305
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.342
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.232.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 1031 9.7 %
Rwork0.276 9595 -
obs--90.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4udpg_pg.parudpg_pg.top

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