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- PDB-1on8: Crystal structure of mouse alpha-1,4-N-acetylhexosaminyltransfera... -

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Entry
Database: PDB / ID: 1on8
TitleCrystal structure of mouse alpha-1,4-N-acetylhexosaminyltransferase (EXTL2) with UDP and GlcUAb(1-3)Galb(1-O)-naphthalenelmethanol an acceptor substrate analog
ComponentsAlpha-1,4-N-acetylhexosaminyltransferase EXTL2
KeywordsTRANSFERASE / Rossmann fold / DXD motif
Function / homology
Function and homology information


UDP-N-acetylgalactosamine metabolic process / alpha-1,4-N-acetylgalactosaminyltransferase activity / glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity / glucuronosyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase / glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity / N-acetylglucosamine metabolic process / glycosaminoglycan binding / manganese ion binding / endoplasmic reticulum membrane / endoplasmic reticulum ...UDP-N-acetylgalactosamine metabolic process / alpha-1,4-N-acetylgalactosaminyltransferase activity / glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity / glucuronosyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase / glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity / N-acetylglucosamine metabolic process / glycosaminoglycan binding / manganese ion binding / endoplasmic reticulum membrane / endoplasmic reticulum / nucleoplasm / cytosol
Similarity search - Function
Glycosyl transferase 64 domain / Glycosyl transferase family 64 domain / 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
: / URIDINE-5'-DIPHOSPHATE / Exostosin-like 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPedersen, L.C. / Dong, J. / Taniguchi, F. / Kitagawa, H. / Krahn, J.M. / Pedersen, L.G. / Sugahara, K. / Negishi, M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of an alpha-1,4-N-acetylhexosaminyltransferase (EXTL2), a member of the exostosin gene family involved in heparan sulfate biosynthesis
Authors: Pedersen, L.C. / Dong, J. / Taniguchi, F. / Kitagawa, H. / Krahn, J.M. / Pedersen, L.G. / Sugahara, K. / Negishi, M.
History
DepositionFeb 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / 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.type_symbol / _chem_comp.name / _chem_comp.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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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 2.1Aug 16, 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
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS NOT KNOWN.
Remark 600HETEROGEN THERE IS NO ELECTRON DENSITY FOR THE NAPTHALENELMETHANOL MOIETY.
Remark 999SEQUENCE ALTHOUGH THE CATALYTIC DOMAIN CONTAINING RESIDUES 38-330 WERE CLONED INTO THE EXPRESSION ...SEQUENCE ALTHOUGH THE CATALYTIC DOMAIN CONTAINING RESIDUES 38-330 WERE CLONED INTO THE EXPRESSION SYSTEM, THE EXACT N-TERMINI OF THE FINAL PRODUCT IS NOT KNOWN DUE TO CLEAVAGE OF THE FUSION PROTEIN WITH A NON-SPECIFIC PROTEASE. HOWEVER THERE IS ELECTRON DENSITY STARTING AT RESIDUE 62.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
B: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,54810
Polymers66,7932
Non-polymers1,7558
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-34 kcal/mol
Surface area21080 Å2
MethodPISA
2
A: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
B: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
hetero molecules

A: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
B: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
hetero molecules

A: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
B: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
hetero molecules

A: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
B: Alpha-1,4-N-acetylhexosaminyltransferase EXTL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,19040
Polymers267,1708
Non-polymers7,02032
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area45210 Å2
ΔGint-239 kcal/mol
Surface area65570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.157, 125.157, 83.692
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Detailsnot known

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Alpha-1,4-N-acetylhexosaminyltransferase EXTL2 / Alpha-GalNAcT EXTL2 / EXT-related protein 2 / Exostosin-like 2


Mass: 33396.312 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: EXTL2 OR EXTR2 / Plasmid: pMAL-2c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9ES89, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Polysaccharide beta-D-glucopyranuronic acid-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 356.280 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpAb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2122A-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpA]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 103 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3000, MgCl2, cacodylate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMHEPES1droppH7.5
2100 mM1dropNaCl
30.1 Msodium cacodylate1reservoirpH7.5
410-12 %PEG30001reservoir
5200 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 16, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 18492 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 33.9 Å2 / Rsym value: 0.095 / Net I/σ(I): 11.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 4 / Num. unique all: 1835 / Rsym value: 0.393 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 112343 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.393

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Processing

Software
NameVersionClassification
CNS1refinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb code: 1OMX

1omx


Resolution: 2.7→19.98 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.254 889 4.9 %RANDOM
Rwork0.192 ---
all0.195 19019 --
obs0.192 18130 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.6595 Å2 / ksol: 0.338551 e/Å3
Displacement parametersBiso mean: 30.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2--0.83 Å20 Å2
3----1.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4188 0 108 97 4393
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.522.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 140 4.9 %
Rwork0.263 2733 -
obs--93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2EDO_ION.PARAMWATER.TOP
X-RAY DIFFRACTION3UDP2.PAREDO.TOP
X-RAY DIFFRACTION4GAG.PARUDP2.TOP
X-RAY DIFFRACTION5WATER_REP.PARAMGAG.TOP
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

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