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- PDB-5ajp: Crystal structure of the active form of GalNAc-T2 in complex with... -

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Basic information

Entry
Database: PDB / ID: 5ajp
TitleCrystal structure of the active form of GalNAc-T2 in complex with UDP and the glycopeptide MUC5AC-13
Components
  • MUCIN
  • POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2
KeywordsTRANSFERASE / GALNAC-T2 / AFM / SAXS / LECTIN DOMAIN / COARSE-GRAINED MODEL / GLYCOPEPTIDES / INACTIVE FORM / ACTIVE FORM / COMPACT FORM / EXTENDED FORM
Function / homology
Function and homology information


: / : / mucus layer / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via N-acetyl-galactosamine / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis ...: / : / mucus layer / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via N-acetyl-galactosamine / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / protein O-linked glycosylation / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / extracellular matrix structural constituent / Golgi cisterna membrane / positive regulation of immunoglobulin production / Dectin-2 family / extracellular matrix / protein maturation / Golgi lumen / manganese ion binding / carbohydrate binding / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / plasma membrane
Similarity search - Function
N-acetylgalactosaminyltransferase / WxxW domain / Mucin-2 protein WxxW repeating region / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. ...N-acetylgalactosaminyltransferase / WxxW domain / Mucin-2 protein WxxW repeating region / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Glycosyltransferase 2-like / Glycosyl transferase family 2 / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / 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 / 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
2-acetamido-2-deoxy-alpha-D-galactopyranose / : / URIDINE-5'-DIPHOSPHATE / Mucin-5AC / Polypeptide N-acetylgalactosaminyltransferase 2 / Mucin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLira-Navarrete, E. / delasRivas, M. / Companon, I. / Pallares, M.C. / Kong, Y. / Iglesias-Fernandez, J. / Bernardes, G.J.L. / Peregrina, J.M. / Rovira, C. / Bernado, P. ...Lira-Navarrete, E. / delasRivas, M. / Companon, I. / Pallares, M.C. / Kong, Y. / Iglesias-Fernandez, J. / Bernardes, G.J.L. / Peregrina, J.M. / Rovira, C. / Bernado, P. / Bruscolini, P. / Clausen, H. / Lostao, A. / Corzana, F. / Hurtado-Guerrero, R.
CitationJournal: Nat.Commun. / Year: 2015
Title: Dynamic Interplay between Catalytic and Lectin Domains of Galnac-Transferases Modulates Protein O-Glycosylation.
Authors: Lira-Navarrete, E. / De Las Rivas, M. / Companon, I. / Pallares, M.C. / Kong, Y. / Iglesias-Fernandez, J. / Bernardes, G.J.L. / Peregrina, J.M. / Rovira, C. / Bernado, P. / Bruscolini, P. / ...Authors: Lira-Navarrete, E. / De Las Rivas, M. / Companon, I. / Pallares, M.C. / Kong, Y. / Iglesias-Fernandez, J. / Bernardes, G.J.L. / Peregrina, J.M. / Rovira, C. / Bernado, P. / Bruscolini, P. / Clausen, H. / Lostao, A. / Corzana, F. / Hurtado-Guerrero, R.
History
DepositionFeb 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _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.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.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.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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2
B: MUCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,06926
Polymers66,3712
Non-polymers2,69824
Water11,007611
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-238.2 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.266, 87.266, 178.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-2112-

HOH

21A-2165-

HOH

31A-2166-

HOH

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Components

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AB

#1: Protein POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2 / POLYPEPTIDE GALNAC TRANSFERASE 2 / GALNAC-T2 / PP-GANTASE 2 / PROTEIN-UDP ...POLYPEPTIDE GALNAC TRANSFERASE 2 / GALNAC-T2 / PP-GANTASE 2 / PROTEIN-UDP ACETYLGALACTOSAMINYLTRANSFERASE 2 / UDP-GALNAC\:POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2 / POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2 SOLUBLE FORM


Mass: 64824.703 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): SMD1168
References: UniProt: Q10471, polypeptide N-acetylgalactosaminyltransferase
#2: Protein/peptide MUCIN


Mass: 1546.632 Da / Num. of mol.: 1 / Fragment: RESIDUES 65-79
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): SMD1168 / References: UniProt: Q14886, UniProt: P98088*PLUS
#6: 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


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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 , 4 types, 634 molecules

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


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.98 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 79709 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.1
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.9 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D0T

4d0t


Resolution: 1.65→89.29 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.196 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18558 2187 2.7 %RANDOM
Rwork0.15598 ---
obs0.15682 77496 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.104 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2---0.75 Å20 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 1.65→89.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4061 0 145 611 4817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194313
X-RAY DIFFRACTIONr_bond_other_d0.0010.023980
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.985867
X-RAY DIFFRACTIONr_angle_other_deg0.83139153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4623.398206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1115722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2111539
X-RAY DIFFRACTIONr_chiral_restr0.0940.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021013
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6322.1662044
X-RAY DIFFRACTIONr_mcbond_other1.6312.1652043
X-RAY DIFFRACTIONr_mcangle_it2.3933.2442554
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.822.642269
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 161 -
Rwork0.24 5645 -
obs--98.41 %
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)
10.0127-0.00650.01130.4326-0.07820.14230.01420.0017-0.01030.0197-0.0262-0.0404-0.02420.0070.0120.031-0.0051-0.01990.00630.00340.01569.757813.54250.2182
20.0051-0.0628-0.00840.8997-0.35113.26530.00350.0012-0.0020.06250.01980.0075-0.1069-0.201-0.02340.04050.0062-0.01750.02740.00860.01363.98728.72758.7583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 569
2X-RAY DIFFRACTION2B2 - 16

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