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- PDB-5foe: Crystal structure of the C. elegans Protein O-fucosyltransferase ... -

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Entry
Database: PDB / ID: 5foe
TitleCrystal structure of the C. elegans Protein O-fucosyltransferase 2 (CePOFUT2) double mutant (R298K-R299K) in complex with GDP and the human TSR1 from thrombospondin 1
ComponentsGDP-fucose protein O-fucosyltransferase 2,Thrombospondin-1
KeywordsTRANSFERASE / POFUT2 / WATERS / FUSION PROTEIN / AFM / ITC / GLYCOSYLTRANSFERASE / SITE-DIRECTED MUTAGENESIS / MOLECULAR DYNAMICS / TSR1
Function / homology
Function and homology information


O-glycosylation of TSR domain-containing proteins / negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / collagen V binding / negative regulation of dendritic cell antigen processing and presentation / negative regulation of nitric oxide mediated signal transduction / peptide-O-fucosyltransferase / protein O-linked glycosylation via fucose / peptide-O-fucosyltransferase activity / negative regulation of sprouting angiogenesis / chronic inflammatory response ...O-glycosylation of TSR domain-containing proteins / negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / collagen V binding / negative regulation of dendritic cell antigen processing and presentation / negative regulation of nitric oxide mediated signal transduction / peptide-O-fucosyltransferase / protein O-linked glycosylation via fucose / peptide-O-fucosyltransferase activity / negative regulation of sprouting angiogenesis / chronic inflammatory response / negative regulation of endothelial cell chemotaxis / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of long-chain fatty acid import across plasma membrane / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / fucose metabolic process / positive regulation of transforming growth factor beta1 production / engulfment of apoptotic cell / fibrinogen complex / negative regulation of focal adhesion assembly / peptide cross-linking / low-density lipoprotein particle binding / Signaling by PDGF / platelet alpha granule / negative regulation of interleukin-12 production / positive regulation of chemotaxis / negative regulation of plasminogen activation / fibrinogen binding / negative regulation of cell migration involved in sprouting angiogenesis / positive regulation of macrophage activation / transforming growth factor beta binding / sprouting angiogenesis / proteoglycan binding / negative regulation of endothelial cell migration / positive regulation of fibroblast migration / extracellular matrix structural constituent / negative regulation of receptor guanylyl cyclase signaling pathway / endopeptidase inhibitor activity / Syndecan interactions / phosphatidylserine binding / negative regulation of interleukin-10 production / positive regulation of transforming growth factor beta receptor signaling pathway / response to testosterone / negative regulation of endothelial cell proliferation / positive regulation of macrophage chemotaxis / fibroblast growth factor binding / behavioral response to pain / fibronectin binding / negative regulation of blood vessel endothelial cell migration / response to magnesium ion / positive regulation of phosphorylation / positive regulation of endothelial cell apoptotic process / negative regulation of cell-matrix adhesion / negative regulation of tumor necrosis factor production / positive regulation of blood coagulation / negative regulation of fibrinolysis / positive regulation of blood vessel endothelial cell migration / response to unfolded protein / Integrin cell surface interactions / response to mechanical stimulus / response to glucose / nitric oxide-cGMP-mediated signaling / laminin binding / positive regulation of smooth muscle cell proliferation / extracellular matrix / positive regulation of endothelial cell migration / response to progesterone / platelet alpha granule lumen / secretory granule / response to endoplasmic reticulum stress / negative regulation of angiogenesis / positive regulation of translation / sarcoplasmic reticulum / negative regulation of extrinsic apoptotic signaling pathway / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / response to calcium ion / cellular response to growth factor stimulus / integrin binding / positive regulation of reactive oxygen species metabolic process / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / cell migration / Platelet degranulation / heparin binding / : / cellular response to heat / protease binding / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / positive regulation of MAPK cascade / immune response / positive regulation of cell migration / endoplasmic reticulum lumen / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation
Similarity search - Function
GDP-fucose protein O-fucosyltransferase 2-like / GDP-fucose protein O-fucosyltransferase / GDP-fucose protein O-fucosyltransferase / Thrombospondin, C-terminal / Thrombospondin, type 3 repeat / Thrombospondin C-terminal region / Thrombospondin type-3 (TSP3) repeat profile. / Thrombospondin C-terminal domain profile. / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat ...GDP-fucose protein O-fucosyltransferase 2-like / GDP-fucose protein O-fucosyltransferase / GDP-fucose protein O-fucosyltransferase / Thrombospondin, C-terminal / Thrombospondin, type 3 repeat / Thrombospondin C-terminal region / Thrombospondin type-3 (TSP3) repeat profile. / Thrombospondin C-terminal domain profile. / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat / : / Thrombospondin N-terminal -like domains. / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Thrombospondin-1 / GDP-fucose protein O-fucosyltransferase 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsValero-Gonzalez, J. / Leonhard-Melief, C. / Lira-Navarrete, E. / Jimenez-Oses, G. / Hernandez-Ruiz, C. / Pallares, M.C. / Yruela, I. / Vasudevan, D. / Lostao, A. / Corzana, F. ...Valero-Gonzalez, J. / Leonhard-Melief, C. / Lira-Navarrete, E. / Jimenez-Oses, G. / Hernandez-Ruiz, C. / Pallares, M.C. / Yruela, I. / Vasudevan, D. / Lostao, A. / Corzana, F. / Takeuchi, H. / Haltiwanger, R.S. / Hurtado-Guerrero, R.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: A Proactive Role of Water Molecules in Acceptor Recognition of Thrombospondin Type 1 Repeats by Protein-O-Fucosyltransferase 2
Authors: Valero-Gonzalez, J. / Leonhard-Melief, C. / Lira-Navarrete, E. / Jimenez-Oses, G. / Hernandez-Ruiz, C. / Pallares, M.C. / Yruela, I. / Vasudevan, D. / Lostao, A. / Corzana, F. / Takeuchi, H. ...Authors: Valero-Gonzalez, J. / Leonhard-Melief, C. / Lira-Navarrete, E. / Jimenez-Oses, G. / Hernandez-Ruiz, C. / Pallares, M.C. / Yruela, I. / Vasudevan, D. / Lostao, A. / Corzana, F. / Takeuchi, H. / Haltiwanger, R.S. / Hurtado-Guerrero, R.
History
DepositionNov 19, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Mar 30, 2016Group: Database references
Revision 1.4Mar 15, 2017Group: Source and taxonomy
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Jan 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 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GDP-fucose protein O-fucosyltransferase 2,Thrombospondin-1
B: GDP-fucose protein O-fucosyltransferase 2,Thrombospondin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,98016
Polymers115,0302
Non-polymers1,94914
Water9,566531
1
A: GDP-fucose protein O-fucosyltransferase 2,Thrombospondin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4908
Polymers57,5151
Non-polymers9757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GDP-fucose protein O-fucosyltransferase 2,Thrombospondin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4908
Polymers57,5151
Non-polymers9757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.026, 67.447, 90.411
Angle α, β, γ (deg.)90.00, 116.07, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9974, -0.07215, 0.009094), (-0.07126, 0.9945, 0.07619), (-0.01454, 0.07534, -0.9971)
Vector: 26.31, -5.701, 38.02)

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Components

#1: Protein GDP-fucose protein O-fucosyltransferase 2,Thrombospondin-1 / Patterning defective protein 2 / Peptide-O-fucosyltransferase 2 / O-FucT-2


Mass: 57515.227 Da / Num. of mol.: 2 / Mutation: YES,YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata), (gene. exp.) Homo sapiens (human)
Gene: pad-2, K10G9.3, THBS1, TSP, TSP1 / Plasmid: PPICZALPHAA / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): X33
References: UniProt: Q8WR51, UniProt: P07996, peptide-O-fucosyltransferase
#2: 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
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsWE MADE A DOUBLE MUTANT OF CEPOFUT2. THIS WAS R298K-R299K. THE NUMBERING OF HSTSR1 IN THE PDB DOES ...WE MADE A DOUBLE MUTANT OF CEPOFUT2. THIS WAS R298K-R299K. THE NUMBERING OF HSTSR1 IN THE PDB DOES NOT CORRESPOND WITH ITS NUMBERING IN THE HUMAN THROMBOSPONDIN 1. HOWEVER, THIS IS EXPLAINED IN THE MANUSCRIPT, WHICH IS ALMOST ACCEPTED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.82 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / 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: 1.98→20 Å / Num. obs: 283636 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.2
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AP5

4ap5


Resolution: 1.98→81.21 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.769 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24607 1852 2.8 %RANDOM
Rwork0.20044 ---
obs0.20168 64467 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.795 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20.42 Å2
2--0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.98→81.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7150 0 124 531 7805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197476
X-RAY DIFFRACTIONr_bond_other_d0.0040.026847
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.95610113
X-RAY DIFFRACTIONr_angle_other_deg1.079315747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7285863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37223.444392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.347151276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8531564
X-RAY DIFFRACTIONr_chiral_restr0.0890.21045
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028357
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021839
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_it1.4642.1353455
X-RAY DIFFRACTIONr_mcbond_other1.4642.1343454
X-RAY DIFFRACTIONr_mcangle_it2.3693.1914311
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6622.3624021
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: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 132 -
Rwork0.269 4733 -
obs--99.9 %
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)
10.5245-0.36760.10240.7858-0.130.1097-0.0119-0.01920.0636-0.01090.0006-0.11060.01080.00190.01130.21310.0069-0.08990.03820.02540.077822.706822.5933.0842
21.15490.28890.17780.67310.13050.1272-0.03360.17370.04240.05230.0149-0.02160.0224-0.09270.01880.2005-0.0497-0.06530.1814-0.00960.02892.173425.80336.5892
31.4150.6414-1.11530.3049-0.47983.8722-0.09090.2913-0.0150.0250.1179-0.02630.2915-0.2274-0.0270.27940.0082-0.0760.13550.01340.029711.347815.1347-14.5227
40.8515-0.2137-0.7230.2039-0.42973.2915-0.0353-0.0897-0.1476-0.06720.04480.05950.24650.0941-0.00950.2229-0.0291-0.05920.0656-0.02030.086414.149217.712954.3295
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 426
2X-RAY DIFFRACTION2B40 - 425
3X-RAY DIFFRACTION3A1003 - 1051
4X-RAY DIFFRACTION4B1003 - 1051

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