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- PDB-6xl8: Crystal structure of 3-O-Sulfotransferase isoform 3 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6xl8
TitleCrystal structure of 3-O-Sulfotransferase isoform 3 in complex with 8mer oligosaccharide with no 6S sulfation
ComponentsHeparan sulfate glucosamine 3-O-sulfotransferase 3A1
KeywordsTRANSFERASE / sulfotransferase / enzyme / PAPS / Heparan sulfate
Function / homology
Function and homology information


[heparan sulfate]-glucosamine 3-sulfotransferase 3 / [heparan sulfate]-glucosamine 3-sulfotransferase 3 activity / [heparan sulfate]-glucosamine 3-sulfotransferase 1 activity / heparan sulfate proteoglycan biosynthetic process, enzymatic modification / HS-GAG biosynthesis / glycosaminoglycan biosynthetic process / sulfotransferase activity / branching involved in ureteric bud morphogenesis / Golgi membrane / membrane
Similarity search - Function
Heparan sulfate sulfotransferase / Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / IODIDE ION / P-NITROPHENOL / Heparan sulfate glucosamine 3-O-sulfotransferase 3A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsPedersen, L.C. / Liu, J. / Wander, R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA ES102645 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL094463 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL144970 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128484 United States
CitationJournal: Rsc Chem Biol / Year: 2021
Title: Deciphering the substrate recognition mechanisms of the heparan sulfate 3- O -sulfotransferase-3.
Authors: Wander, R. / Kaminski, A.M. / Xu, Y. / Pagadala, V. / Krahn, J.M. / Pham, T.Q. / Liu, J. / Pedersen, L.C.
History
DepositionJun 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 3A1
B: Heparan sulfate glucosamine 3-O-sulfotransferase 3A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,65018
Polymers62,4322
Non-polymers5,21816
Water1,27971
1
A: Heparan sulfate glucosamine 3-O-sulfotransferase 3A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4777
Polymers31,2161
Non-polymers2,2616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heparan sulfate glucosamine 3-O-sulfotransferase 3A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,17311
Polymers31,2161
Non-polymers2,95710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.217, 147.469, 51.037
Angle α, β, γ (deg.)90.000, 94.350, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Heparan sulfate glucosamine 3-O-sulfotransferase 3A1 / Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1 / h3-OST-3A


Mass: 31215.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HS3ST3A1, 3OST3A1, HS3ST3A, UNQ2551/PRO6180 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: Q9Y663, [heparan sulfate]-glucosamine 3-sulfotransferase 3

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Sugars , 2 types, 2 molecules

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


Type: oligosaccharide / Mass: 1430.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,6,5/[a2122h-1a_1-5_2*NSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O][a2122A-1b_1-5]/1-2-1-2-1-3/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1,2-deoxy-Glcp]{[(4+1)][a-L-6-deoxy-Idop2SO3]{[(4+1)][a-D-2-deoxy-Glcp]{[(4+1)][a-L-6-deoxy-Idop2SO3]{[(4+1)][a-D-2-deoxy-Glcp]{[(4+1)][b-D-GlcpA]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo- ...beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 1606.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,7,6/[a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-3-2-3-2-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpA]{[(4+1)][a-D-2-deoxy-Glcp]{[(4+1)][a-L-6-deoxy-Idop2SO3]{[(4+1)][a-D-2-deoxy-Glcp]{[(4+1)][a-L-6-deoxy-Idop2SO3]{[(4+1)][a-D-2-deoxy-Glcp]{[(4+1)][b-D-GlcpA]{}}}}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 85 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#6: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#7: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 14mg/ml 3ost3a in 25mM Tris pH 7.5, 125mM NaCl, 4mM PAP and 5mM 8mer oligosaccharide Reservoir: 0.2M KI and 20%PEG3350
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.514 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 16, 2019 / Details: varimaxHF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 22494 / % possible obs: 94.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 37.53 Å2 / Rpim(I) all: 0.089 / Rrim(I) all: 0.163 / Rsym value: 0.136 / Net I/σ(I): 7.3
Reflection shellResolution: 2.34→2.38 Å / Redundancy: 2 % / Num. unique obs: 923 / CC1/2: 0.718 / CC star: 0.914 / Rpim(I) all: 0.326 / Rrim(I) all: 0.523 / Rsym value: 0.405 / % possible all: 77.2

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T8U

1t8u


Resolution: 2.34→21.7 Å / SU ML: 0.3203 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 29.6902
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2709 1116 4.97 %
Rwork0.2162 21346 -
obs0.2189 22462 94.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.62 Å2
Refinement stepCycle: LAST / Resolution: 2.34→21.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4109 0 256 71 4436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114467
X-RAY DIFFRACTIONf_angle_d0.93886080
X-RAY DIFFRACTIONf_chiral_restr0.0487696
X-RAY DIFFRACTIONf_plane_restr0.0034741
X-RAY DIFFRACTIONf_dihedral_angle_d14.21331624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.440.35961070.27882144X-RAY DIFFRACTION76.02
2.44-2.570.37151380.27262583X-RAY DIFFRACTION91.4
2.57-2.730.30651460.26552805X-RAY DIFFRACTION99.26
2.73-2.940.31521460.25672834X-RAY DIFFRACTION100
2.94-3.240.30071490.25212804X-RAY DIFFRACTION99.97
3.24-3.70.28631450.23062766X-RAY DIFFRACTION97.85
3.7-4.660.2531300.18532605X-RAY DIFFRACTION91.44
4.66-21.70.20411550.16792805X-RAY DIFFRACTION98.47
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)
10.0957911652918-0.630841649209-0.03476289416350.4597060580750.5111474309380.662559787238-0.06406435418450.0517907283733-0.0594480585737-0.155728773288-0.0540183657329-0.0861680356637-0.0285520201540.02454143286696.53450563468E-80.32803046025-0.04270021773070.009404247458130.3349508257620.007498419167650.2683397465634.8762266138-51.8998556226104.239268557
20.0585879370829-0.01056141823640.00572643543423-0.0410428682240.2093410289540.0495728255938-0.2563865606360.06241427913250.744196545802-0.4268513320760.03921731227180.0905258107413-0.3569179102060.1164166925960.0008687097674610.399991858833-0.0546383712302-0.06004191487510.373093686728-0.06893958482020.26451185847529.9130066039-55.684813298298.196112926
30.4559570341260.866567525477-0.03422117722211.212882514010.5375615433970.349141745235-0.1081729679440.01091914794810.0231190288762-0.09153973050050.0340843208491-0.1054334807030.10730020064-0.00821811841419-2.63593083788E-60.309177362777-0.02303722775570.001672132137680.2956896644530.03273848127440.23204370088734.8378434865-44.1937412762114.246616701
4-0.131491723162-0.1748058766720.2692822501930.5656555666970.2888387152270.1179961207860.1575937150910.01048087954130.06849677980051.09702180442-0.2523754050.0963039078943-0.157173853197-0.107814286556-0.01731729463820.335460770327-0.0737372134242-0.01721876352460.3423262527390.01226689751970.36527078865545.2637939078-41.5004194087134.235240334
50.1582112285190.04441385817420.03176052004120.00492330100305-0.09747936123010.1927644985410.08743059315490.285027667691-0.291760889089-0.0852441518988-0.10613410518-0.6404484740020.2978824250470.266889190498-0.0127186616820.373707785299-0.018090269834-0.06941985112050.303281309434-0.02795062968790.38696760755139.6706961221-36.6142228163126.138347416
6-0.03801493496470.0303118191230.1478607188790.0440092246043-0.05685955461430.0808850553544-0.09891639586430.0163926552280.0515779997311-0.3901550335940.0569046234506-0.4435979089930.2366774309580.3618278291816.86671600705E-70.432270744076-0.03769822462270.002421761877680.3306685546250.0646766947770.42000853857229.9215800032-34.4697028433110.883428624
70.459008296839-0.1150478495160.2665859322630.0844515375246-0.180956068318-0.119962670328-0.1432623767030.118708370680.2395681372280.0573568478178-0.1107364333090.33657522689-0.247560695029-0.45110417866-7.32993547416E-70.311510194118-0.017074942761-0.002424923878550.341809150395-0.03028657614960.44142039435620.6987945817-49.8904132538114.385753339
80.165351109441-0.1007050604530.05422228554810.08175172861110.273461192090.128556590112-0.00517668239110.0506867398346-0.05622142618220.03957124740160.04743663935690.0732400271597-0.0396670753261-0.0220726428729-1.38120906487E-60.32226329168-0.0548060930377-0.0198252468610.323825688542-0.04933562768910.40592861298821.3852523865-62.6950932505115.84308277
90.193227281869-0.3735635446280.2822261520580.390732645905-0.08492437097530.0726422418040.1213976023040.0410154225669-0.06317009841870.0975754969377-0.07418376480280.1932815414120.05751451450790.0586635803033-4.58871408197E-70.365030043207-0.006009522746020.02866462696480.27828982622-0.004228382901120.28438694497132.4627542326-62.2457308046120.702111384
100.0388255441026-0.06654003988340.1990106700030.6667963346820.6159710810640.08236065760070.31501142808-0.62104800871-0.09689901844730.127259408835-0.1142806383770.5039364690220.187679526444-0.3615889357710.02675640635480.391106146122-0.0604203371581-0.003637816570620.4178133175-0.03520395131550.26223104080326.2015488137-37.8599925113128.343484992
110.4506893088570.4401269299480.0955109348110.22097638556-0.2708567107130.8167381640880.01815578279780.112834470592-0.1612316128850.017496144536-0.0005097354362750.1289253362540.03143539766320.2299138756421.2630053786E-80.2512425272910.04050642640470.02545877967490.247824092097-0.03974332636270.22139853289120.4443184296-86.5107161619105.378461272
120.1546329021180.0998085016124-0.2358722959940.196336145624-0.09104303848240.2584049150530.0411833135536-0.7381213449280.5889405357691.010548868720.399917736667-0.138634027817-0.001152557435430.3275034334870.00765127871330.396199304074-0.0145438349006-0.04304735957920.425275178772-0.04903237388870.36385415506124.5320036517-86.3669431084115.519116902
131.021710778160.261985726186-0.159517328193-0.237018936537-0.0934418805610.00327753203885-0.04281415691770.01040957482320.03854906217670.0710699814914-0.2052086519260.05655901195620.003080912897570.02542324675331.73679161031E-70.34391583587-0.008722212668760.005335519542660.317026836462-0.01826224800710.27144205765113.3874437895-91.2368324224104.747371182
140.565886948688-0.403804518049-0.1631335083180.783065133901-0.151039702305-0.168728579582-0.09463600240090.003087626940390.0977727939483-0.07764188678840.09214588142770.126934649631-0.1386068223120.05465185718891.2119652965E-80.254547264538-0.03044355163310.01056790482310.288987852967-0.05532568826320.26480781749415.5609688636-96.904261838680.9493747948
15-0.004441132666080.197160117589-0.229612042440.232739494073-0.6354329759211.216336727010.114580339643-0.223347827038-0.849634898282-0.30799847398-0.0989004474469-0.08208915979521.221516747220.01034016931280.02715591736070.275702666446-0.07798496416820.08360574755170.4496662033920.03934904401470.279656361014.81993958772-96.2358641467101.784666718
160.329538918095-0.0480646094640.0120780147525-0.103172030672-0.2719902093030.518498146142-0.0906420259858-0.2158147437380.2304004398510.0001315004976340.002892194885220.147505424953-0.09185658330330.144259909676-1.91478267168E-70.29772224645-0.0073248576822-0.006013762856960.260093858111-0.03661120551830.2848841875697.5932732471-78.721408948299.7762026165
170.2187601498250.03055750709590.4578443293750.1881816540070.8623923008790.442106006139-0.165070944924-0.0363017203989-0.129430928826-0.1203820846840.179255764361-0.0341586325276-0.1560381957690.291900817858-2.39570197164E-70.320310358673-0.04244760527850.02927330237310.314187271802-0.02422491480280.37446392762720.3821368141-73.560987412392.853262976
180.561174615866-0.6491642163460.3402054746520.00605268215731-0.2881200709020.107546109289-0.1112289765870.130029712676-0.0307343135348-0.061208714887-0.1066570305590.232215988454-0.0600667077498-0.384876542227-1.18766006735E-70.293546137914-0.02504513920270.02239916226240.348995239027-0.05468905534630.4160084534451.54226313262-90.029978433985.4248779504
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 149 through 202 )AA149 - 2021 - 54
22chain 'A' and (resid 203 through 215 )AA203 - 21555 - 67
33chain 'A' and (resid 216 through 258 )AA216 - 25868 - 110
44chain 'A' and (resid 259 through 276 )AA259 - 276111 - 128
55chain 'A' and (resid 277 through 290 )AA277 - 290129 - 142
66chain 'A' and (resid 291 through 303 )AA291 - 303143 - 155
77chain 'A' and (resid 304 through 329 )AA304 - 329156 - 181
88chain 'A' and (resid 330 through 349 )AA330 - 349182 - 201
99chain 'A' and (resid 350 through 376 )AA350 - 376202 - 228
1010chain 'A' and (resid 377 through 406 )AA377 - 406229 - 258
1111chain 'B' and (resid 149 through 195 )BC149 - 1951 - 47
1212chain 'B' and (resid 196 through 210 )BC196 - 21048 - 62
1313chain 'B' and (resid 211 through 244 )BC211 - 24463 - 96
1414chain 'B' and (resid 245 through 290 )BC245 - 29097 - 142
1515chain 'B' and (resid 291 through 303 )BC291 - 303143 - 155
1616chain 'B' and (resid 304 through 329 )BC304 - 329156 - 181
1717chain 'B' and (resid 330 through 376 )BC330 - 376182 - 228
1818chain 'B' and (resid 377 through 405 )BC377 - 405229 - 257

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