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- PDB-2vs3: THE BINDING OF UDP-GALACTOSE BY AN ACTIVE SITE MUTANT OF alpha-1,... -

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Basic information

Entry
Database: PDB / ID: 2vs3
TitleTHE BINDING OF UDP-GALACTOSE BY AN ACTIVE SITE MUTANT OF alpha-1,3 GALACTOSYLTRANSFERASE (alpha3GT)
ComponentsN-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE
KeywordsTRANSFERASE / MANGANESE / GLYCOPROTEIN / METAL-BINDING / ACTIVE-SITE MUTANT / GLYCOSYLTRANSFERASE / N-ACETYL LACTOSAMINE / SIGNAL-ANCHOR / TRANSMEMBRANE / GOLGI APPARATUS / GT / UDP / MEMBRANE / ALPHA3GT / GALACTOSE / ALPHA-3GT
Function / homology
Function and homology information


N-acetyllactosaminide 3-alpha-galactosyltransferase / N-acetyllactosaminide 3-alpha-galactosyltransferase activity / Golgi cisterna / lipid glycosylation / Golgi cisterna membrane / glycosyltransferase activity / protein glycosylation / vesicle / carbohydrate metabolic process / Golgi apparatus / metal ion binding
Similarity search - Function
Glycosyl transferase, family 6 / Glycosyltransferase family 6 / 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
N-acetyl-alpha-lactosamine / : / URIDINE-5'-DIPHOSPHATE / N-acetyllactosaminide alpha-1,3-galactosyltransferase
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTumbale, P. / Jamaluddin, H. / Thiyagarajan, N. / Brew, K. / Acharya, K.R.
CitationJournal: Biochemistry / Year: 2008
Title: Structural Basis of Udp-Galactose Binding by Alpha- 1,3-Galactosyltransferase (Alpha3Gt): Role of Negative Charge on Aspartic Acid 316 in Structure and Activity.
Authors: Tumbale, P. / Jamaluddin, H. / Thiyagarajan, N. / Brew, K. / Acharya, K.R.
History
DepositionApr 18, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle / struct_conn
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_conn_type / 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.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE
B: N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8638
Polymers68,1782
Non-polymers1,6856
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-11.6 kcal/mol
Surface area29630 Å2
MethodPQS
Unit cell
Length a, b, c (Å)45.116, 94.380, 94.940
Angle α, β, γ (deg.)90.00, 99.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE / GALACTOSYLTRANSFERASE / UDP-GALACTOSE\: BETA-D-GALACTOSYL-1 / 4-N-ACETYL-D-GLUCOSAMINIDE ALPHA-1 / ...GALACTOSYLTRANSFERASE / UDP-GALACTOSE\: BETA-D-GALACTOSYL-1 / 4-N-ACETYL-D-GLUCOSAMINIDE ALPHA-1 / 3-GALACTOSYLTRANSFERASE / ALPHA-1 / 3 GALACTOSYLTRANSFERASE


Mass: 34089.180 Da / Num. of mol.: 2 / Fragment: RESIDUES 80-368 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14769, N-acetyllactosaminide 3-alpha-galactosyltransferase
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-lactosamine


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 383.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: N-acetyl-alpha-lactosamine
DescriptorTypeProgram
DGalpb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: 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
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 316 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 316 TO ASN

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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: 2.93 Å3/Da / Density % sol: 58.1 % / Description: NONE
Crystal growpH: 8
Details: PROTEIN: 10 MM UDP-GAL, 10 MM MNCL2, 10 MM N-ACETYLLACTOSAMINE, MOTHER LIQUOR: 5-10 % PEG 6000, 0.1 M TRIS-HCL PH 8.0, 5-14 % MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 4, 2006 / Details: MIRRORS
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 39855 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.5 / % possible all: 86.2

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4V

1k4v


Resolution: 2.2→35.18 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 403590.17 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.224 743 2.1 %RANDOM
Rwork0.215 ---
obs0.215 36204 90.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.3312 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.44 Å20 Å20.24 Å2
2--2.88 Å20 Å2
3----7.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→35.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4786 0 104 424 5314
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.33
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.24 90 1.7 %
Rwork0.277 5128 -
obs--78.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3UDP-NLC-GOL-GOL-2403.PARUDP-NLC-GOL-GOL-2403.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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