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- PDB-2ffv: Human ppGalNAcT-2 complexed with manganese and UDP -

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Basic information

Entry
Database: PDB / ID: 2ffv
TitleHuman ppGalNAcT-2 complexed with manganese and UDP
ComponentsPolypeptide N-acetylgalactosaminyltransferase 2
KeywordsTRANSFERASE / ppGalNAcT / mucin / glycosyltransferase
Function / homology
Function and homology information


protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / O-glycan processing / O-linked glycosylation of mucins / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / protein O-linked glycosylation / Golgi cisterna membrane ...protein O-linked glycosylation via threonine / protein O-linked glycosylation via serine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / O-glycan processing / O-linked glycosylation of mucins / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / protein O-linked glycosylation / Golgi cisterna membrane / protein maturation / manganese ion binding / carbohydrate binding / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular region / membrane
Similarity search - Function
N-acetylgalactosaminyltransferase / 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 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A ...N-acetylgalactosaminyltransferase / 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 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE / Polypeptide N-acetylgalactosaminyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsFritz, T.A.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Dynamic Association between the Catalytic and Lectin Domains of Human UDP-GalNAc:Polypeptide {alpha}-N-Acetylgalactosaminyltransferase-2
Authors: Fritz, T.A. / Raman, J. / Tabak, L.A.
History
DepositionDec 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1786
Polymers114,2602
Non-polymers9184
Water00
1
A: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5893
Polymers57,1301
Non-polymers4592
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5893
Polymers57,1301
Non-polymers4592
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Polypeptide N-acetylgalactosaminyltransferase 2
B: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules

A: Polypeptide N-acetylgalactosaminyltransferase 2
B: Polypeptide N-acetylgalactosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,35612
Polymers228,5194
Non-polymers1,8368
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area15440 Å2
ΔGint-105 kcal/mol
Surface area73650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)153.228, 153.228, 110.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is either one of the two monomers

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Components

#1: Protein Polypeptide N-acetylgalactosaminyltransferase 2 / E.C.2.4.1.41 / ppGalNAcT-2 / Protein-UDP acetylgalactosaminyltransferase 2 / UDP-GalNAc:polypeptide N- ...ppGalNAcT-2 / Protein-UDP acetylgalactosaminyltransferase 2 / UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 2 / Polypeptide GalNAc transferase 2 / GalNAc-T2 / pp-GaNTase 2


Mass: 57129.844 Da / Num. of mol.: 2 / Fragment: Catalytic and lectin domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Invitrogen pPIC9 vector with TEV-protease-cleavable, N-terminal engineered 6His tag
Gene: GALNT2 / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1168
References: UniProt: Q10471, polypeptide N-acetylgalactosaminyltransferase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: 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

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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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG, Hepes, MnCl2, EDTA, mercaptoethanol, UDP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97472 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97472 Å / Relative weight: 1
ReflectionResolution: 2.75→49.1 Å / Num. all: 34646 / Num. obs: 34265 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 64.6 Å2

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASERphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Separate catalytic domains of PDB entry 1XHB in which nonconserved residues were changed to alanine

1xhb


Resolution: 2.75→49.1 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2290873.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1731 5.1 %RANDOM
Rwork0.225 ---
all0.2251 34646 --
obs0.2251 34265 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.276 Å2 / ksol: 0.334354 e/Å3
Displacement parametersBiso mean: 44.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.9 Å20 Å20 Å2
2--1.2 Å20 Å2
3----4.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.75→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7780 0 52 0 7832
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it5.351.5
X-RAY DIFFRACTIONc_mcangle_it8.392
X-RAY DIFFRACTIONc_scbond_it6.72
X-RAY DIFFRACTIONc_scangle_it9.662.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.427 265 4.9 %
Rwork0.367 5192 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramwater.top
X-RAY DIFFRACTION3udp.param2ion.top
X-RAY DIFFRACTION4udp.topo2

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