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- PDB-6wmo: Human poly-N-acetyl-lactosamine synthase structure demonstrates a... -

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Basic information

Entry
Database: PDB / ID: 6wmo
TitleHuman poly-N-acetyl-lactosamine synthase structure demonstrates a modular assembly of catalytic subsites for GT-A glycosyltransferases
ComponentsN-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
KeywordsTRANSFERASE / Glycosyltransferase / GT-A fold / poly LacNAc synthesis
Function / homology
Function and homology information


N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase / : / UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity / poly-N-acetyllactosamine biosynthetic process / keratan sulfate biosynthetic process / Keratan sulfate biosynthesis / O-glycan processing / O-linked glycosylation of mucins / protein O-linked glycosylation ...N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase / : / UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity / poly-N-acetyllactosamine biosynthetic process / keratan sulfate biosynthetic process / Keratan sulfate biosynthesis / O-glycan processing / O-linked glycosylation of mucins / protein O-linked glycosylation / cellular response to leukemia inhibitory factor / axon guidance / sensory perception of smell / Golgi membrane
Similarity search - Function
Glycosyl transferase, family 31 / Galactosyltransferase
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKadirvelraj, R. / Wood, Z.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1P01GM107012-02 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Comparison of human poly-N-acetyl-lactosamine synthase structure with GT-A fold glycosyltransferases supports a modular assembly of catalytic subsites.
Authors: Kadirvelraj, R. / Yang, J.Y. / Kim, H.W. / Sanders, J.H. / Moremen, K.W. / Wood, Z.A.
History
DepositionApr 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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 beta-1,3-N-acetylglucosaminyltransferase 2
B: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,95219
Polymers84,4402
Non-polymers4,51117
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Ultracentrifugation: Velocity
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10510 Å2
ΔGint24 kcal/mol
Surface area28110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.190, 109.280, 147.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 56 through 147 or resid 149...
21(chain B and (resid 56 through 147 or resid 149...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 56 through 147 or resid 149...A56 - 147
121(chain A and (resid 56 through 147 or resid 149...A149
131(chain A and (resid 56 through 147 or resid 149...A151 - 211
141(chain A and (resid 56 through 147 or resid 149...A308 - 332
151(chain A and (resid 56 through 147 or resid 149...A334 - 35
161(chain A and (resid 56 through 147 or resid 149...A365 - 392
211(chain B and (resid 56 through 147 or resid 149...B56 - 147
221(chain B and (resid 56 through 147 or resid 149...B149
231(chain B and (resid 56 through 147 or resid 149...B151 - 211
241(chain B and (resid 56 through 147 or resid 149...B213 - 260
251(chain B and (resid 56 through 147 or resid 149...B56 - 392
261(chain B and (resid 56 through 147 or resid 149...B33
271(chain B and (resid 56 through 147 or resid 149...B334 - 392

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2 / Beta-1 / 3-N-acetylglucosaminyltransferase 1 / Beta3Gn-T1 / 3-galactosyltransferase 7 / b3Gal-T7 / ...Beta-1 / 3-N-acetylglucosaminyltransferase 1 / Beta3Gn-T1 / 3-galactosyltransferase 7 / b3Gal-T7 / Beta-3-Gx-T7 / UDP-Gal:beta-GlcNAc beta-1 / UDP-GlcNAc:betaGal beta-1 / 3-N-acetylglucosaminyltransferase 2 / Beta3Gn-T2 / UDP-galactose:beta-N-acetylglucosamine beta-1


Mass: 42220.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B3GNT2, B3GALT7, B3GNT1 / Production host: Homo sapiens (human)
References: UniProt: Q9NY97, N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase

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Sugars , 3 types, 7 molecules

#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 545.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-1/a3-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 240 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mg
#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C9H14N2O12P2 / Comment: UDP*YM
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24% PEG3350, 6% Ethylene glycol, 100 mM Hepes pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 21, 2016
RadiationMonochromator: Rosenbaum-Rock double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→37.848 Å / Num. obs: 67358 / % possible obs: 99.7 % / Redundancy: 14.071 % / Biso Wilson estimate: 37 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.063 / Χ2: 1.036 / Net I/σ(I): 24.4 / Num. measured all: 947780 / Scaling rejects: 43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2% possible allRrim(I) all
1.85-1.99.8991.0147310.44996.4
1.9-1.9512.6981.8347990.805100
1.95-2.0114.5792.5646920.867100
2.01-2.0714.5613.6745130.94100
2.07-2.1414.3835.1544300.96100
2.14-2.2114.3536.8742820.977100
2.21-2.2914.3279.0341460.987100
2.29-2.3914.44111.7939610.992100
2.39-2.4914.66715.3738070.994100
2.49-2.6214.88520.0936280.997100
2.62-2.7614.92425.2835060.998100
2.76-2.9214.90132.9533140.999100
2.92-3.1314.8341.631080.999100
3.13-3.3814.78751.3129100.999100
3.38-3.714.63264.0327161100
3.7-4.1414.52672.924281100
4.14-4.7714.35578.9121961100
4.77-5.8514.1178.4818471100
5.85-8.2713.67378.7414841100
8.27-37.84812.28582.81860198.70.027

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WMM

6wmm


Resolution: 1.85→37.848 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.71
RfactorNum. reflection% reflection
Rfree0.2115 3367 5 %
Rwork0.1828 --
obs0.1842 67291 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.7 Å2 / Biso mean: 50.3168 Å2 / Biso min: 20.94 Å2
Refinement stepCycle: final / Resolution: 1.85→37.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5261 0 294 230 5785
Biso mean--55.13 48.22 -
Num. residues----638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015772
X-RAY DIFFRACTIONf_angle_d0.9287843
X-RAY DIFFRACTIONf_chiral_restr0.057877
X-RAY DIFFRACTIONf_plane_restr0.006972
X-RAY DIFFRACTIONf_dihedral_angle_d11.7743427
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2987X-RAY DIFFRACTION7.059TORSIONAL
12B2987X-RAY DIFFRACTION7.059TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.87640.36361290.3552246796
1.8764-1.90440.39171330.305261899
1.9044-1.93420.31961490.27622664100
1.9342-1.96590.2971320.24442600100
1.9659-1.99980.29471460.23682654100
1.9998-2.03620.23641300.21572608100
2.0362-2.07530.22841430.20312643100
2.0753-2.11770.23431400.20012642100
2.1177-2.16370.22961390.2022655100
2.1637-2.21410.23261450.18642636100
2.2141-2.26940.22271300.1812646100
2.2694-2.33080.24061400.18642653100
2.3308-2.39930.24561410.19012660100
2.3993-2.47680.24591410.19162642100
2.4768-2.56530.23211400.18152659100
2.5653-2.6680.22111340.18542699100
2.668-2.78940.22981420.17462659100
2.7894-2.93640.22451430.1942647100
2.9364-3.12030.24811440.19272696100
3.1203-3.3610.2211390.18992679100
3.361-3.6990.20081460.17042732100
3.699-4.23360.17731420.1492711100
4.2336-5.33160.16051450.15732762100
5.3316-37.8480.19691540.19152892100
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)
13.3212-0.18720.762.72680.26886.0432-0.20690.3504-0.3464-1.01770.0740.21970.7414-0.37140.15730.9301-0.07210.03490.3942-0.0780.419716.4604-24.4401-41.7151
25.3888-5.8296-3.13667.27742.66993.4765-0.36480.0549-0.59640.07870.03760.6440.7119-0.29840.29620.4884-0.13410.00930.2997-0.0590.306811.4157-18.157-32.6431
33.42221.38690.72383.02320.35397.14-0.0405-0.02460.30440.1015-0.12130.3971-0.2999-0.33440.15060.29080.03970.05140.2464-0.02540.275911.8326.9613-26.9056
40.86182.3764-1.63977.0412-5.77535.1152-0.16170.16760.1452-0.22350.36730.46740.2078-0.6907-0.1760.431-0.05330.03730.3773-0.03570.335410.1009-0.9764-24.2154
52.1035-0.9504-0.30735.6465-0.644.8617-0.02670.03760.066-0.10360.08480.3410.3757-0.3863-0.03640.2467-0.08640.0030.331-0.00970.28358.0424-3.3443-28.0389
63.81591.29570.85777.8749-2.93283.2234-0.0510.29780.1981-0.4471-0.03110.0449-0.40360.00870.09130.45590.01840.07760.3062-0.02170.202520.486410.1634-34.4638
72.1656-0.19750.21334.2142-1.39323.3489-0.03750.2854-0.1437-0.5075-0.0781-0.25910.2770.25790.11890.49440.00710.09840.3779-0.02490.213124.0437-6.9335-39.7061
85.6551.89111.60526.68842.36624.153-0.0809-0.16870.0040.04810.0487-0.8694-0.01491.6854-0.01830.3114-0.03450.05910.65920.03030.366734.20095.0185-30.4239
94.2449-3.0838-0.52035.95620.67664.61080.0087-0.21330.7199-0.4850.187-0.6829-0.84520.5186-0.14290.4694-0.15120.04190.437-0.03480.308128.595113.5628-21.8329
104.60350.86971.01763.05950.16954.6956-0.1696-0.47890.6890.38790.0525-1.0083-0.86830.67010.11210.4843-0.0803-0.13350.446-0.12360.704630.554614.635512.1798
110.56650.73290.71035.58080.21555.7078-0.0559-0.085-0.0233-0.0572-0.0040.22060.2579-0.55090.04770.1641-0.02840.00970.3189-0.02320.25338.6738-6.11972.0082
123.97262.7279-1.78116.6334-1.98327.3672-0.006-0.01180.1087-0.2577-0.00870.0644-0.2111-0.3071-0.02420.18080.06470.01860.2699-0.06670.238210.51053.1992-1.5651
132.37240.87020.7323.67051.16923.22930.1696-0.2929-0.47870.56470.066-1.07040.45060.348-0.12420.30090.0624-0.11860.39510.00430.543823.9788-6.676810.8496
145.1347-0.37393.35535.78062.04125.78360.06720.1169-0.52280.3530.0355-0.47371.07290.2848-0.08130.52460.04610.11210.3286-0.10740.498717.5677-18.6298-4.8064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 54 through 113 )A54 - 113
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 131 )A114 - 131
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 170 )A132 - 170
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 194 )A171 - 194
5X-RAY DIFFRACTION5chain 'A' and (resid 195 through 234 )A195 - 234
6X-RAY DIFFRACTION6chain 'A' and (resid 235 through 261 )A235 - 261
7X-RAY DIFFRACTION7chain 'A' and (resid 262 through 343 )A262 - 343
8X-RAY DIFFRACTION8chain 'A' and (resid 344 through 365 )A344 - 365
9X-RAY DIFFRACTION9chain 'A' and (resid 366 through 397 )A366 - 397
10X-RAY DIFFRACTION10chain 'B' and (resid 56 through 131 )B56 - 131
11X-RAY DIFFRACTION11chain 'B' and (resid 132 through 170 )B132 - 170
12X-RAY DIFFRACTION12chain 'B' and (resid 171 through 216 )B171 - 216
13X-RAY DIFFRACTION13chain 'B' and (resid 217 through 369 )B217 - 369
14X-RAY DIFFRACTION14chain 'B' and (resid 370 through 392 )B370 - 392

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