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

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Basic information

Entry
Database: PDB / ID: 6wmm
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 / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity / keratan sulfate proteoglycan biosynthetic process / poly-N-acetyllactosamine biosynthetic process / N-acetyl-beta-D-glucosaminide beta-(1,3)-galactosyltransferase activity / Keratan sulfate biosynthesis / protein O-linked GalNAcylation / O-linked glycosylation of mucins / protein O-linked glycosylation / axon guidance ...N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity / keratan sulfate proteoglycan biosynthetic process / poly-N-acetyllactosamine biosynthetic process / N-acetyl-beta-D-glucosaminide beta-(1,3)-galactosyltransferase activity / Keratan sulfate biosynthesis / protein O-linked GalNAcylation / O-linked glycosylation of mucins / protein O-linked glycosylation / axon guidance / cellular response to leukemia inhibitory factor / 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 / SAD / Resolution: 1.548 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 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)88,26317
Polymers85,0032
Non-polymers3,25915
Water8,611478
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Ultracentrifugation: Velocity
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.730, 110.920, 147.400
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 57 through 71 or resid 91...
21(chain B and (resid 57 through 128 or resid 130...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 57 through 71 or resid 91...A57 - 71
121(chain A and (resid 57 through 71 or resid 91...A91 - 128
131(chain A and (resid 57 through 71 or resid 91...A130 - 169
141(chain A and (resid 57 through 71 or resid 91...A196 - 211
151(chain A and (resid 57 through 71 or resid 91...A57 - 394
161(chain A and (resid 57 through 71 or resid 91...A230 - 320
171(chain A and (resid 57 through 71 or resid 91...A57 - 394
181(chain A and (resid 57 through 71 or resid 91...A376 - 38
191(chain A and (resid 57 through 71 or resid 91...A7
1101(chain A and (resid 57 through 71 or resid 91...A389 - 394
211(chain B and (resid 57 through 128 or resid 130...B57 - 128
221(chain B and (resid 57 through 128 or resid 130...B130 - 169
231(chain B and (resid 57 through 128 or resid 130...B171 - 183
241(chain B and (resid 57 through 128 or resid 130...B185 - 194
251(chain B and (resid 57 through 128 or resid 130...B196 - 211
261(chain B and (resid 57 through 128 or resid 130...B213 - 228
271(chain B and (resid 57 through 128 or resid 130...B230 - 320
281(chain B and (resid 57 through 128 or resid 130...B322 - 374
291(chain B and (resid 57 through 128 or resid 130...B376 - 387
2101(chain B and (resid 57 through 128 or resid 130...B389 - 394

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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: 42501.574 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 , 2 types, 4 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 2
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, 489 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% PEG3350, 16% Ethylene glycol, 100 mM Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.95 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 15, 2016
RadiationMonochromator: Rosenbaum-Rock / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.548→35.862 Å / Num. obs: 224051 / % possible obs: 99.4 % / Redundancy: 7.592 % / Biso Wilson estimate: 22.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.093 / Χ2: 1.082 / Net I/σ(I): 12.97
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2% possible allRmerge(I) obsRrim(I) all
1.55-1.597.0350.89154670.43692.6
1.59-1.637.6161.14162980.524100
1.63-1.687.6341.6158090.676100
1.68-1.737.6492.14152950.784100
1.73-1.797.6742.85148630.856100
1.79-1.857.6943.86143750.913100
1.85-1.927.6945.35139220.948100
1.92-27.727.32132970.972100
2-2.097.7089.75128380.985100
2.09-2.197.73112.66122340.9911000.17
2.19-2.317.67915.62116650.994100
2.31-2.457.71318.74110160.9961000.1
2.45-2.627.68922.31103020.997100
2.62-2.827.62726.396620.9971000.07
2.82-3.097.55930.9388490.998100
3.09-3.467.45335.6480450.9991000.04
3.46-3.997.32439.770480.999100
3.99-4.897.41642.3459630.999100
4.89-6.927.38741.9645960.999100
6.92-35.8627.27743.1725070.99899.80.037

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XSCALEdata scaling
PHASER2.6.0phasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.548→35.86 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.39
RfactorNum. reflection% reflection
Rfree0.1984 11184 5.01 %
Rwork0.1771 --
obs0.1782 223262 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.93 Å2 / Biso mean: 31.4559 Å2 / Biso min: 12.73 Å2
Refinement stepCycle: final / Resolution: 1.548→35.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5338 0 208 478 6024
Biso mean--33.45 40.11 -
Num. residues----648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0175772
X-RAY DIFFRACTIONf_angle_d1.3467842
X-RAY DIFFRACTIONf_chiral_restr0.095854
X-RAY DIFFRACTIONf_plane_restr0.009986
X-RAY DIFFRACTIONf_dihedral_angle_d14.7692206
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2962X-RAY DIFFRACTION6.559TORSIONAL
12B2962X-RAY DIFFRACTION6.559TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5485-1.56610.42573050.392582982
1.5661-1.58450.32893700.33957085100
1.5845-1.60380.33393800.32957115100
1.6038-1.62410.32323750.32067159100
1.6241-1.64550.35813690.30347034100
1.6455-1.6680.29473800.27547150100
1.668-1.69190.27153720.25657097100
1.6919-1.71710.293720.25357120100
1.7171-1.74390.2453810.23947108100
1.7439-1.77250.27473720.23117073100
1.7725-1.80310.2463810.23117179100
1.8031-1.83590.2533750.21387059100
1.8359-1.87120.22053800.20497153100
1.8712-1.90940.22283760.18977055100
1.9094-1.95090.23283810.1877195100
1.9509-1.99630.22023720.17627031100
1.9963-2.04620.20063730.17687165100
2.0462-2.10150.20833740.17287096100
2.1015-2.16330.20433790.17227095100
2.1633-2.23320.21113690.16887130100
2.2332-2.3130.2013730.16367158100
2.313-2.40550.1953700.16477057100
2.4055-2.5150.20413740.1787137100
2.515-2.64760.19223760.16357099100
2.6476-2.81340.19183670.16377142100
2.8134-3.03050.19193820.1657134100
3.0305-3.33530.16453770.16047080100
3.3353-3.81740.17963800.15267113100
3.8174-4.80770.13653720.14067118100
4.8077-35.860.19983770.17997112100
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)
11.48750.1423-0.40461.4796-0.20072.0541-0.15030.1479-0.3886-0.2163-0.0356-0.28180.43170.26070.06110.24780.04640.06330.2237-0.01760.279124.576345.274362.5361
21.2472-0.4575-0.22622.698-0.12183.28960.00920.0171-0.0441-0.04-0.00020.10240.1106-0.1404-0.04710.1014-0.0081-0.01290.1975-0.01130.148710.589555.73175.4202
31.5937-0.5387-0.20042.1622-0.06211.89720.01330.09050.1687-0.1419-0.0531-0.4121-0.20810.2610.00760.153-0.01450.01910.25670.03070.212524.318361.816162.2529
45.03350.686-0.70392.44031.32674.8120.1360.04730.6432-0.0125-0.0932-0.3234-0.60070.34970.00650.3595-0.0615-0.01490.2468-0.0090.33318.073576.103877.1561
53.7233-1.0893-0.64373.5261.43883.86390.1432-0.54880.45891.0335-0.442-0.1912-0.51920.29650.23350.5311-0.0268-0.07550.293-0.03790.283821.010578.8393121.1545
62.05171.21920.88982.7250.99141.2988-0.1525-0.21290.26180.0993-0.06260.4261-0.3002-0.20360.20290.32050.0339-0.01560.1917-0.02580.255413.063378.4015108.2829
70.8601-0.57140.21422.4502-0.94763.20820.01640.0225-0.07790.01740.00290.19980.0144-0.1343-0.0160.1333-0.0111-0.01810.1534-0.01010.160711.780551.701499.3645
80.99180.2131-0.18772.12910.21222.6267-0.02410.03780.03010.00260.00070.2007-0.1181-0.1951-0.0030.17040.0305-0.0130.16830.00030.18718.682758.9775101.4381
91.3663-0.3214-0.14860.9712-0.29762.2416-0.009-0.0098-0.05370.1359-0.01140.04780.0588-0.0340.02820.2279-0.0045-0.0150.1498-0.00040.186421.087945.7376107.8567
100.9529-0.2559-0.15443.1872-0.05011.5085-0.0116-0.04420.05580.1899-0.0567-0.2717-0.04150.08890.0820.2102-0.0125-0.0490.18180.00410.160224.53963.0298113.1788
114.3186-2.5975-2.96864.42623.28728.57020.08990.03360.0958-0.17150.079-0.5251-0.12770.9443-0.19730.2032-0.0368-0.04020.27170.03970.291233.427351.942106.2334
122.35731.48770.09373.73730.35792.11810.0474-0.0968-0.2282-0.0162-0.0151-0.50030.36160.3860.00390.22220.08360.00850.24450.02140.226628.977841.999195.6402
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 57 through 154 )A57 - 154
2X-RAY DIFFRACTION2chain 'A' and (resid 155 through 216 )A155 - 216
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 365 )A217 - 365
4X-RAY DIFFRACTION4chain 'A' and (resid 366 through 394 )A366 - 394
5X-RAY DIFFRACTION5chain 'B' and (resid 52 through 70 )B52 - 70
6X-RAY DIFFRACTION6chain 'B' and (resid 71 through 131 )B71 - 131
7X-RAY DIFFRACTION7chain 'B' and (resid 132 through 194 )B132 - 194
8X-RAY DIFFRACTION8chain 'B' and (resid 195 through 234 )B195 - 234
9X-RAY DIFFRACTION9chain 'B' and (resid 235 through 261 )B235 - 261
10X-RAY DIFFRACTION10chain 'B' and (resid 262 through 340 )B262 - 340
11X-RAY DIFFRACTION11chain 'B' and (resid 341 through 365 )B341 - 365
12X-RAY DIFFRACTION12chain 'B' and (resid 366 through 397 )B366 - 397

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