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- PDB-3ioi: Crystal structure of the Fucosylgalactoside alpha N-acetylgalacto... -

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Basic information

Entry
Database: PDB / ID: 3ioi
TitleCrystal structure of the Fucosylgalactoside alpha N-acetylgalactosaminyltransferase (GTA, cisAB mutant L266G, G268A) in complex with a novel UDP-Gal derived inhibitor (1GW)
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE / GTA / ABO / cisAB mutant / AA(Gly)B / ROSSMANN FOLD / INHIBITOR / SEMI-CLOSED CONFORMATION / BLOOD GROUP ANTIGEN / GLYCOPROTEIN / GLYCOSYLTRANSFERASE / GOLGI APPARATUS / MANGANESE / MEMBRANE / METAL-BINDING / POLYMORPHISM / SECRETED / SIGNAL-ANCHOR / TRANSMEMBRANE
Function / homology
Function and homology information


fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding ...fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region
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
Chem-1GW / : / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsPesnot, T. / Jorgensen, R. / Palcic, M.M. / Wagner, G.K.
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: Structural and mechanistic basis for a new mode of glycosyltransferase inhibition.
Authors: Pesnot, T. / Jorgensen, R. / Palcic, M.M. / Wagner, G.K.
History
DepositionAug 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 13, 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 1.5Sep 6, 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: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4814
Polymers34,6541
Non-polymers8273
Water4,035224
1
A: Histo-blood group ABO system transferase
hetero molecules

A: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9638
Polymers69,3082
Non-polymers1,6556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5280 Å2
ΔGint-59 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.160, 148.440, 79.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Histo-blood group ABO system transferase / NAGAT / Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / ...NAGAT / Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase / Histo-blood group A transferase / A transferase / Glycoprotein-fucosylgalactoside alpha-galactosyltransferase / Fucosylglycoprotein 3-alpha-galactosyltransferase / Histo-blood group B transferase / B transferase / Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase soluble form


Mass: 34654.008 Da / Num. of mol.: 1 / Fragment: Extracellular catalytic domain / Mutation: L266G, G268A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Plasmid: PCW DELTA 1AC / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase, fucosylgalactoside 3-alpha-galactosyltransferase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1GW / 5-(2-FORMYLTHIEN-5-YL)-URIDINE-5'-DIPHOSPHATE-ALPHA-D-GALACTOSE


Mass: 676.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N2O18P2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM MOPS pH 7, 50-200 mM ammonium sulfate, 50 mM MnCl2, and 6-9% PEG-3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.90772 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: May 29, 2009
Details: Multilayer mirror, curved to focus in the vertical (R = 400 m)
RadiationMonochromator: Bent Si (220) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90772 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. obs: 54487 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 11.07 % / Biso Wilson estimate: 22.001 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 17.34
Reflection shellResolution: 1.45→1.6 Å / Redundancy: 7.25 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 2.9 / Num. measured obs: 99444 / Num. unique all: 13715 / Num. unique obs: 13715 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.75 Å
Translation2.5 Å19.75 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER1.3.3phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RIT

2rit


Resolution: 1.45→19.644 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.907 / SU ML: 0.03 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.175 1634 3 %RANDOM
Rwork0.159 ---
obs0.16 54482 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.529 Å2 / ksol: 0.46 e/Å3
Displacement parametersBiso max: 109.67 Å2 / Biso mean: 20.78 Å2 / Biso min: 6.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.616 Å20 Å20 Å2
2--0.012 Å2-0 Å2
3---1.605 Å2
Refinement stepCycle: LAST / Resolution: 1.45→19.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2241 0 49 224 2514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012408
X-RAY DIFFRACTIONf_angle_d1.4183286
X-RAY DIFFRACTIONf_chiral_restr0.084349
X-RAY DIFFRACTIONf_plane_restr0.007413
X-RAY DIFFRACTIONf_dihedral_angle_d17.619931
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.4930.271340.2454292442699
1.493-1.5410.2651330.224360449399
1.541-1.5960.2281350.18243534488100
1.596-1.660.1981330.16743664499100
1.66-1.7350.1691370.15643974534100
1.735-1.8270.1841370.14743894526100
1.827-1.9410.1731350.14243844519100
1.941-2.0910.1541360.13144164552100
2.091-2.3010.1341370.13244144551100
2.301-2.6330.1611380.14444564594100
2.633-3.3150.1781380.15644714609100
3.315-19.6460.1621410.1664550469198
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)
10.1092-0.5650.45541.6673-0.29071.29120.2662-0.049-0.03480.0549-0.2679-0.30180.13350.3501-0.00520.16830.02880.00720.2191-0.00150.18898.643511.2313-31.8055
20.79270.2755-0.1386-0.27440.1290.7632-0.02250.0271-0.12720.00890.0396-0.08230.1578-0.0405-0.01220.0955-0.0018-0.00980.0649-0.00510.10861.67939.3421-15.4419
31.75770.82190.27230.94890.0970.0641-0.06060.2613-0.0641-0.06380.11910.002-0.02180.0144-0.05650.08420.0037-0.00050.12440.01390.09313.465721.3069-24.2778
40.99370.07860.1670.552-0.27521.16250.0743-0.15890.01680.070.0286-0.087-0.0309-0.0114-0.06040.0955-0.0237-0.01840.1149-0.00630.084120.762224.40260.3758
50.14830.22980.03970.65440.07681.48590.04850.0932-0.0774-0.0139-0.0103-0.1677-0.03830.171-0.02810.082-0.0002-0.00520.10390.00110.116123.279720.5642-11.1499
60.3841-0.2003-0.09521.04250.3125.220.07380.07730.0203-0.15090.0977-0.1772-0.40360.1965-0.17830.1073-0.01590.02270.0907-0.02380.09820.460530.3913-9.1818
73.9462.1690.1781.90530.07610.54130.1757-0.1479-0.03960.3123-0.0891-0.2116-0.33710.2468-0.07960.1932-0.0449-0.00850.1625-0.01870.136326.663929.96283.8832
81.0403-0.6094-0.70990.85530.00021.38040.1178-0.23930.17460.0937-0.1141-0.0131-0.09380.4187-0.02020.0788-0.01560.0040.1749-0.01050.079227.704928.0184-12.0958
91.49970.1399-0.93890.8692-0.38830.0439-0.0014-0.19870.06840.28490.18630.3049-0.1529-0.0206-0.14440.26340.01040.0480.19530.00020.180216.791532.11335.1799
102.0904-1.01220.55111.60181.05041.16320.4056-0.62730.744-0.1065-0.2007-0.1273-0.1777-0.0567-0.12860.239-0.01330.0670.3615-0.15170.38779.203234.94481.8048
113.4052-0.3623-0.92684.35634.68662.08640.0789-0.50080.8066-0.3213-0.0349-0.0884-0.4781-0.1234-0.02050.15950.00620.00870.1464-0.04790.242311.925436.1419-9.525
120.3810.21850.2804-0.0124-0.17990.91640.06770.0024-0.07720.0057-0.0484-0.00490.12880.0774-0.02530.1160.0004-0.02420.09420.02130.116118.3816.2408-4.837
130.76830.0108-0.25320.14690.22880.150.0185-0.0458-0.16280.086-0.0535-0.01640.0432-0.02360.03820.0955-0.0059-0.01110.07860.01380.10484.435613.8522-6.7239
140.96640.2376-0.45121.75220.77791.28270.0751-0.3326-0.00810.3454-0.11220.37870.13-0.39040.01750.1674-0.03120.04770.22070.02290.1479-7.190116.38346.8792
150.61480.1444-0.04630.29190.25780.09860.0492-0.0707-0.01310.0507-0.045-0.01020.0506-0.0318-0.0070.1009-0.0116-0.0060.0990.01620.0943.906919.0479-4.5602
161.1444-0.6734-0.95840.72790.12961.17390.15850.11840.24820.0264-0.0869-0.0324-0.37-0.2789-0.07710.15030.02420.02020.1319-0.00450.13081.637232.0702-2.6281
170.22520.40930.47062.11030.0826-3.51690.0466-0.29970.07030.88040.1529-0.1310.01170.1249-0.1620.3397-00.03120.2468-0.04520.1097-1.409128.619812.7101
181.0109-0.085-0.23190.8064-0.21140.0490.0354-0.1774-0.06790.14530.0070.0137-0.0335-0.0995-0.02910.0967-0.00260.00130.13490.01740.0831-0.48920.4469-1.2064
190.2456-0.37450.1475-0.246-0.10291.3099-0.02690.026-0.12380.0767-0.07340.02490.2150.01110.06830.1561-0.0063-0.02090.07960.03110.133413.4695.9194-4.5662
201.13090.06330.8358-0.0982-0.49773.13060.0781-0.0469-0.25220.0514-0.1373-0.14230.26640.16270.00170.1240.0053-0.04160.10830.02340.138317.08839.5764-5.4206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 65:80)A65 - 80
2X-RAY DIFFRACTION2(chain A and resid 81:97)A81 - 97
3X-RAY DIFFRACTION3(chain A and resid 98:113)A98 - 113
4X-RAY DIFFRACTION4(chain A and resid 114:132)A114 - 132
5X-RAY DIFFRACTION5(chain A and resid 133:145)A133 - 145
6X-RAY DIFFRACTION6(chain A and resid 146:151)A146 - 151
7X-RAY DIFFRACTION7(chain A and resid 152:161)A152 - 161
8X-RAY DIFFRACTION8(chain A and resid 162:169)A162 - 169
9X-RAY DIFFRACTION9(chain A and resid 170:188)A170 - 188
10X-RAY DIFFRACTION10(chain A and resid 189:196)A189 - 196
11X-RAY DIFFRACTION11(chain A and resid 197:207)A197 - 207
12X-RAY DIFFRACTION12(chain A and resid 208:219)A208 - 219
13X-RAY DIFFRACTION13(chain A and resid 220:242)A220 - 242
14X-RAY DIFFRACTION14(chain A and resid 243:260)A243 - 260
15X-RAY DIFFRACTION15(chain A and resid 261:274)A261 - 274
16X-RAY DIFFRACTION16(chain A and resid 275:286)A275 - 286
17X-RAY DIFFRACTION17(chain A and resid 287:298)A287 - 298
18X-RAY DIFFRACTION18(chain A and resid 299:319)A299 - 319
19X-RAY DIFFRACTION19(chain A and resid 320:335)A320 - 335
20X-RAY DIFFRACTION20(chain A and resid 336:346)A336 - 346

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