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- PDB-3uan: Crystal structure of 3-O-sulfotransferase (3-OST-1) with bound PA... -

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Basic information

Entry
Database: PDB / ID: 3uan
TitleCrystal structure of 3-O-sulfotransferase (3-OST-1) with bound PAP and heptasaccharide substrate
ComponentsHeparan sulfate glucosamine 3-O-sulfotransferase 1
KeywordsTRANSFERASE / sulfotransferase / heparan sulfate / alpha/beta motif / co-factor PAPS/PAP / heparan sulfate oligosaccharides / Golgi-localized
Function / homology
Function and homology information


[heparan sulfate]-glucosamine 3-sulfotransferase 1 / HS-GAG biosynthesis / [heparan sulfate]-glucosamine 3-sulfotransferase 1 activity / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / Golgi lumen / Golgi apparatus
Similarity search - Function
Heparan sulfate sulfotransferase / Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / beta-D-glucopyranuronic acid / Heparan sulfate glucosamine 3-O-sulfotransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.844 Å
AuthorsMoon, A.F. / Xu, Y. / Woody, S.M. / Krahn, J.M. / Linhardt, R.J. / Liu, J. / Pedersen, L.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Dissecting the substrate recognition of 3-O-sulfotransferase for the biosynthesis of anticoagulant heparin.
Authors: Moon, A.F. / Xu, Y. / Woody, S.M. / Krahn, J.M. / Linhardt, R.J. / Liu, J. / Pedersen, L.C.
History
DepositionOct 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Apr 25, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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: Heparan sulfate glucosamine 3-O-sulfotransferase 1
B: Heparan sulfate glucosamine 3-O-sulfotransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7857
Polymers62,8082
Non-polymers3,9775
Water4,792266
1
A: Heparan sulfate glucosamine 3-O-sulfotransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3833
Polymers31,4041
Non-polymers1,9792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heparan sulfate glucosamine 3-O-sulfotransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4014
Polymers31,4041
Non-polymers1,9973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.883, 62.168, 86.373
Angle α, β, γ (deg.)90.00, 95.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Heparan sulfate glucosamine 3-O-sulfotransferase 1 / Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 1 / Heparan sulfate 3-O-sulfotransferase 1


Mass: 31403.879 Da / Num. of mol.: 2 / Fragment: 3-O-sulfotransferase isoform 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hs3st1, 3ost, 3ost1 / Plasmid: pGEX4T3 / Production host: Escherichia coli (E. coli)
References: UniProt: O35310, [heparan sulfate]-glucosamine 3-sulfotransferase 1

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Sugars , 3 types, 3 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2- ...2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 1552.272 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/4,6,5/[a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NCC/3=O_6*OSO/3=O/3=O]/1-2-3-2-1-4/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpA]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-GlcpNAc6SO3]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2- ...2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1376.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/4,5,4/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O][a2122A-1b_1-5][a2122h-1a_1-5_2*NCC/3=O_6*OSO/3=O/3=O]/1-2-1-3-4/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-GlcpNAc6SO3]{}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid / Glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 268 molecules

#4: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE / Adenosine 3',5'-bisphosphate


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.5
Details: Crystals of the 3-OST-1/PAP/heptasaccharide complex were obtained using micro-batch technique, by mixing 1.5 mL of the complex (12.9 mg/mL 3-OST-1, 5 mM heptasaccharide, 4 mM PAP, 23.6 mM ...Details: Crystals of the 3-OST-1/PAP/heptasaccharide complex were obtained using micro-batch technique, by mixing 1.5 mL of the complex (12.9 mg/mL 3-OST-1, 5 mM heptasaccharide, 4 mM PAP, 23.6 mM Tris pH 7.5, 142 mM NaCl) was mixed with 2.5 mL of 0.1 M sodium citrate pH 5.5 and 20% PEG 3000. Crystals grew to a usable size after 10 days incubation at room temperature. The crystals were transferred in two steps to a cryoprotectant solution containing 0.1 M sodium citrate pH 5.5, 0.1 M NaCl, 4 mM PAP, 20 mM heptasaccharide, 30% PEG3000, and 7.6% ethylene glycol. , temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.844→25 Å / Num. all: 46408 / Num. obs: 44993 / % possible obs: 96.95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 26.97 Å2 / Rsym value: 0.05 / Net I/σ(I): 21.8
Reflection shellResolution: 1.844→1.88 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.11 / Num. unique all: 2039 / Rsym value: 0.314 / % possible all: 84.6

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPSuitephasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZRH

1zrh


Resolution: 1.844→24.57 Å / SU ML: 0.21 / Cross valid method: Rfree / σ(F): 0 / Phase error: 20.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 2247 4.99 %random
Rwork0.1742 ---
all0.175 46408 --
obs0.175 44993 93.2 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.308 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.5316 Å20 Å23.9567 Å2
2--0.1457 Å2-0 Å2
3----5.6773 Å2
Refinement stepCycle: LAST / Resolution: 1.844→24.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4103 0 236 266 4605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044563
X-RAY DIFFRACTIONf_angle_d0.8386263
X-RAY DIFFRACTIONf_dihedral_angle_d11.971578
X-RAY DIFFRACTIONf_chiral_restr0.056692
X-RAY DIFFRACTIONf_plane_restr0.004767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.844-1.88410.26411050.2461855X-RAY DIFFRACTION65
1.8841-1.92790.22981210.21372354X-RAY DIFFRACTION83
1.9279-1.97610.23441290.19672547X-RAY DIFFRACTION89
1.9761-2.02950.23621350.1942574X-RAY DIFFRACTION90
2.0295-2.08920.231400.18912628X-RAY DIFFRACTION93
2.0892-2.15650.20981430.17962720X-RAY DIFFRACTION95
2.1565-2.23360.23281450.17892703X-RAY DIFFRACTION95
2.2336-2.32290.21531540.1692768X-RAY DIFFRACTION96
2.3229-2.42860.20351390.17452752X-RAY DIFFRACTION97
2.4286-2.55650.20121370.18252805X-RAY DIFFRACTION97
2.5565-2.71650.2251540.1942784X-RAY DIFFRACTION98
2.7165-2.92590.2131400.19872823X-RAY DIFFRACTION98
2.9259-3.21980.22161560.18672817X-RAY DIFFRACTION98
3.2198-3.68430.16721470.16962843X-RAY DIFFRACTION99
3.6843-4.63680.16721470.13552869X-RAY DIFFRACTION99
4.6368-24.57210.20951550.17392904X-RAY DIFFRACTION98
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)
10.8794-0.0862-0.4670.9621-0.19782.5221-0.04950.1236-0.08540.0664-0.0433-0.11450.0937-0.19150.04670.1487-0.0062-0.01220.1378-0.01910.1615.64951.982534.0161
20.28760.0675-0.17380.38040.08530.04650.0321-0.11660.02250.2937-0.11780.04470.1238-0.0640.03280.2484-0.04390.06690.2459-0.00530.19244.82765.999355.8667
30.7899-0.42040.130.3857-0.07640.0959-0.1557-0.33170.13150.29630.1856-0.22750.11710.41730.05470.32590.0645-0.12810.36720.01550.310829.78350.089249.8617
41.29610.2876-0.09720.3836-0.11610.1671-0.3125-0.3427-0.27910.15250.0379-0.0260.4041-0.05150.08560.4275-0.10490.1280.2395-0.00390.25375.8219-8.132151.2802
50.8025-0.76590.43232.26890.22591.9068-0.305-0.41810.29370.28310.1754-0.2708-0.421-0.29850.08830.41850.0369-0.05050.2891-0.02990.282111.2812.087647.8918
61.7826-0.71920.47250.814-0.32162.1317-0.0322-0.08780.17550.1210.0907-0.0952-0.2073-0.0177-0.03190.17570.01710.00150.165-0.0140.195812.734424.2449.3177
70.2063-0.0935-0.13910.187-0.01110.2404-0.08820.0846-0.00760.0610.08460.00310.07910.0945-0.01390.20340.0690.02190.31280.00260.18117.131317.1392-13.3638
80.10910.0470.0130.08920.00490.05350.07530.290.1823-0.28870.0578-0.2483-0.16290.46570.0120.5845-0.2160.1460.37140.1920.617522.317237.1795-4.368
90.80260.19020.67710.561-0.13740.53420.02170.3440.2177-0.1714-0.02730.1372-0.1658-0.00250.01790.2870.11550.00250.38850.06430.2543-0.968928.0164-7.5815
100.06290.10640.14730.55040.0710.34450.02920.08130.2202-0.2313-0.1502-0.32670.04210.19550.05250.26110.06730.08670.41080.03650.395617.268216.8015-4.8823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 1:151 or resid 200:245)
2X-RAY DIFFRACTION2chain A and resid 152:199
3X-RAY DIFFRACTION3chain A and resid 246:275
4X-RAY DIFFRACTION4chain A and resid 276:999
5X-RAY DIFFRACTION5chain C
6X-RAY DIFFRACTION6chain B and (resid 1:151 or resid 200:245)
7X-RAY DIFFRACTION7chain B and resid 152:199
8X-RAY DIFFRACTION8chain B and resid 246:275
9X-RAY DIFFRACTION9chain B and resid 276:999
10X-RAY DIFFRACTION10chain D

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