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- PDB-6pxu: Crystal structure of human GalNAc-T12 bound to a diglycosylated p... -

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Basic information

Entry
Database: PDB / ID: 6pxu
TitleCrystal structure of human GalNAc-T12 bound to a diglycosylated peptide, Mn2+, and UDP
Components
  • GAGATGAGAGYYITPRTGAGA
  • Polypeptide N-acetylgalactosaminyltransferase 12
KeywordsTRANSFERASE / GalNAc-T / mucin-type O-glycosylation / enzyme catalysis / substrate selectivity / colorectal cancer / CRC
Function / homology
Function and homology information


polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / Defective GALNT12 causes CRCS1 / O-glycan processing / O-linked glycosylation of mucins / carbohydrate binding / membrane => GO:0016020 / Golgi membrane / Golgi apparatus / metal ion binding
Similarity search - Function
Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / : / URIDINE-5'-DIPHOSPHATE / Polypeptide N-acetylgalactosaminyltransferase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.007 Å
AuthorsSamara, N.L. / Fernandez, A.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1 ZIA DE000739 05 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM113534 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: The structure of the colorectal cancer-associated enzyme GalNAc-T12 reveals how nonconserved residues dictate its function.
Authors: Fernandez, A.J. / Daniel, E.J.P. / Mahajan, S.P. / Gray, J.J. / Gerken, T.A. / Tabak, L.A. / Samara, N.L.
History
DepositionJul 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.value / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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: Polypeptide N-acetylgalactosaminyltransferase 12
B: Polypeptide N-acetylgalactosaminyltransferase 12
C: GAGATGAGAGYYITPRTGAGA
D: GAGATGAGAGYYITPRTGAGA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,55434
Polymers129,1604
Non-polymers3,39430
Water10,124562
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A: Polypeptide N-acetylgalactosaminyltransferase 12
C: GAGATGAGAGYYITPRTGAGA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,12315
Polymers64,5802
Non-polymers1,54313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-7 kcal/mol
Surface area23880 Å2
MethodPISA
2
B: Polypeptide N-acetylgalactosaminyltransferase 12
D: GAGATGAGAGYYITPRTGAGA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,43119
Polymers64,5802
Non-polymers1,85117
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-4 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.820, 73.123, 74.441
Angle α, β, γ (deg.)113.080, 100.500, 108.230
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 51:60 or resseq 62:66 or resseq...
21(chain B and (resseq 51:60 or resseq 62:66 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 51:60 or resseq 62:66 or resseq...A51 - 60
121(chain A and (resseq 51:60 or resseq 62:66 or resseq...A62 - 66
131(chain A and (resseq 51:60 or resseq 62:66 or resseq...A68 - 79
141(chain A and (resseq 51:60 or resseq 62:66 or resseq...A81 - 82
151(chain A and (resseq 51:60 or resseq 62:66 or resseq...A91 - 114
161(chain A and (resseq 51:60 or resseq 62:66 or resseq...A51 - 600
171(chain A and (resseq 51:60 or resseq 62:66 or resseq...A153
181(chain A and (resseq 51:60 or resseq 62:66 or resseq...A51 - 600
191(chain A and (resseq 51:60 or resseq 62:66 or resseq...A51 - 600
1101(chain A and (resseq 51:60 or resseq 62:66 or resseq...A51 - 600
1111(chain A and (resseq 51:60 or resseq 62:66 or resseq...A51 - 600
1121(chain A and (resseq 51:60 or resseq 62:66 or resseq...A51 - 600
1131(chain A and (resseq 51:60 or resseq 62:66 or resseq...A51 - 600
211(chain B and (resseq 51:60 or resseq 62:66 or resseq...B51 - 60
221(chain B and (resseq 51:60 or resseq 62:66 or resseq...B62 - 66
231(chain B and (resseq 51:60 or resseq 62:66 or resseq...B68 - 79
241(chain B and (resseq 51:60 or resseq 62:66 or resseq...B114
251(chain B and (resseq 51:60 or resseq 62:66 or resseq...B50 - 600
261(chain B and (resseq 51:60 or resseq 62:66 or resseq...B126 - 152
271(chain B and (resseq 51:60 or resseq 62:66 or resseq...B153
281(chain B and (resseq 51:60 or resseq 62:66 or resseq...B50 - 600
291(chain B and (resseq 51:60 or resseq 62:66 or resseq...B50 - 600
2101(chain B and (resseq 51:60 or resseq 62:66 or resseq...B50 - 600
2111(chain B and (resseq 51:60 or resseq 62:66 or resseq...B50 - 600
2121(chain B and (resseq 51:60 or resseq 62:66 or resseq...B50 - 600
2131(chain B and (resseq 51:60 or resseq 62:66 or resseq...B50 - 600

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Components

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Protein / Protein/peptide / Sugars , 3 types, 8 molecules ABCD

#1: Protein Polypeptide N-acetylgalactosaminyltransferase 12 / / Polypeptide GalNAc transferase 12 / pp-GaNTase 12 / Protein-UDP acetylgalactosaminyltransferase 12 ...Polypeptide GalNAc transferase 12 / pp-GaNTase 12 / Protein-UDP acetylgalactosaminyltransferase 12 / UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 12


Mass: 62738.980 Da / Num. of mol.: 2 / Fragment: UNP residues 39-581
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GALNT12 / Production host: Komagataella pastoris (fungus)
References: UniProt: Q8IXK2, polypeptide N-acetylgalactosaminyltransferase
#2: Protein/peptide GAGATGAGAGYYITPRTGAGA


Mass: 1840.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: Sugar
ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 588 molecules

#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium chloride, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 11, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.007→20.03 Å / Num. obs: 163130 / % possible obs: 97 % / Redundancy: 1 % / Biso Wilson estimate: 29.33 Å2 / Rpim(I) all: 0.1 / Rrim(I) all: 0.197 / Χ2: 1.071 / Net I/σ(I): 4.7
Reflection shellResolution: 2.007→2.03 Å / Redundancy: 3.1 % / Num. unique obs: 3795 / CC1/2: 0.339 / Rpim(I) all: 0.903 / % possible all: 89.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FFU

2ffu


Resolution: 2.007→20.027 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.73 / Phase error: 24.8
RfactorNum. reflection% reflection
Rfree0.2189 7888 4.84 %
Rwork0.1711 --
obs0.1734 163130 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.26 Å2 / Biso mean: 42.0352 Å2 / Biso min: 14.66 Å2
Refinement stepCycle: final / Resolution: 2.007→20.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8846 0 206 562 9614
Biso mean--47.91 42.56 -
Num. residues----1086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079397
X-RAY DIFFRACTIONf_angle_d0.98112722
X-RAY DIFFRACTIONf_chiral_restr0.0591322
X-RAY DIFFRACTIONf_plane_restr0.0061657
X-RAY DIFFRACTIONf_dihedral_angle_d21.4435684
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4844X-RAY DIFFRACTION11.365TORSIONAL
12B4844X-RAY DIFFRACTION11.365TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0073-2.030.34282360.2911454285
2.03-2.05390.35482700.285481492
2.0539-2.07890.32022540.2806495892
2.0789-2.10520.31842320.2629485693
2.1052-2.13290.28282420.2565527496
2.1329-2.16210.2692580.2411497896
2.1621-2.19290.25593000.2451532897
2.1929-2.22560.32562740.2448503898
2.2256-2.26030.31382480.2402527897
2.2603-2.29730.28282780.2281510898
2.2973-2.33690.32562400.2247522898
2.3369-2.37930.28783020.2241518698
2.3793-2.4250.25222780.2093521098
2.425-2.47440.23552920.1958520698
2.4744-2.52810.31452880.1997517298
2.5281-2.58680.2352500.2014521098
2.5868-2.65140.2652300.2005527498
2.6514-2.72290.27512380.1967526498
2.7229-2.80280.26472780.1866529698
2.8028-2.8930.25452200.1798522899
2.893-2.99610.24542940.1781521098
2.9961-3.11560.22542460.169531299
3.1156-3.25690.20852780.1679528299
3.2569-3.42780.21192580.154523299
3.4278-3.64130.18952760.1416530699
3.6413-3.92050.18552340.1355529299
3.9205-4.31150.14282660.1215527099
4.3115-4.92730.15192580.1184532099
4.9273-6.17750.17843020.14045282100
6.1775-20.020.16562680.1376528899
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)
17.7337-0.0464-4.95691.07750.1664.94970.1307-0.21170.1995-0.0799-0.0383-0.2188-0.71120.3583-0.09560.5629-0.122-0.02070.2787-0.02290.32343.231919.847614.3269
20.8263-0.1479-0.33250.67820.57992.30990.01720.1724-0.0215-0.1144-0.0760.0311-0.1647-0.01110.05580.17590.00270.00250.2211-0.00170.18-2.74830.11144.4866
34.7358-0.26580.87573.6124-1.83183.2660.14060.75390.3233-0.2397-0.1674-0.0039-0.5143-0.5880.03570.44410.21670.01920.58310.01380.29763.2247-5.3973-31.9939
45.9985-0.32823.5981.44020.27494.23030.40310.0339-0.4627-0.0151-0.1977-0.2560.64160.26-0.23560.39390.01630.01970.22140.06260.372538.4015-43.2511-18.6367
50.9889-0.00790.40280.96080.39451.80550.0026-0.1559-0.00670.0685-0.04120.00190.0256-0.05090.04060.1664-0.0235-0.00450.20730.00280.169233.2779-27.3684-13.472
60.4840.15690.73880.42270.71042.5892-0.0678-0.13950.1443-0.0189-0.13680.0281-0.2246-0.17950.21220.27350.0126-0.04820.3654-0.09940.291835.121-8.31927.9561
75.71990.4542-0.22165.8396-0.51565.5677-0.1247-0.6059-0.35070.13920.2174-0.00120.509-0.5817-0.08320.2875-0.0139-0.01650.376-0.00490.265239.6802-17.641428.1008
86.5338-0.9771-4.63685.20072.01779.63610.4890.7349-0.3079-0.4173-0.30590.0695-0.11680.3498-0.16140.59880.08030.00060.5753-0.03380.27534.84114.7941-6.3703
98.17233.26794.05251.29741.6232.67510.1378-0.51340.51790.7592-0.16530.32770.0213-0.40080.12090.7177-0.09690.12360.7548-0.1470.747345.3494-25.32444.2945
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 51 through 101 )A51 - 101
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 460 )A102 - 460
3X-RAY DIFFRACTION3chain 'A' and (resid 461 through 581 )A461 - 581
4X-RAY DIFFRACTION4chain 'B' and (resid 50 through 101 )B50 - 101
5X-RAY DIFFRACTION5chain 'B' and (resid 102 through 387 )B102 - 387
6X-RAY DIFFRACTION6chain 'B' and (resid 388 through 460 )B388 - 460
7X-RAY DIFFRACTION7chain 'B' and (resid 461 through 581 )B461 - 581
8X-RAY DIFFRACTION8chain 'C' and (resid 5 through 21 )C5 - 21
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 19 )D1 - 19

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