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- PDB-4uzq: STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH O-PALMITOLEO... -

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Basic information

Entry
Database: PDB / ID: 4uzq
TitleSTRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH O-PALMITOLEOYL SERINE - CRYSTAL FORM IX - 1.5A
Components
  • PROTEIN NOTUM HOMOLOG
  • PROTEIN WNT-7A
KeywordsHYDROLASE / ESTERASE / EXTRACELLULAR / ALPHA/BETA HYDROLASE
Function / homology
Function and homology information


postsynapse assembly / positive regulation of excitatory synapse assembly / positive regulation of protein localization to presynapse / skeletal muscle satellite cell activation / regulation of axon diameter / asymmetric protein localization involved in cell fate determination / lens fiber cell development / cerebellar granule cell differentiation / WNT ligand biogenesis and trafficking / oviduct development ...postsynapse assembly / positive regulation of excitatory synapse assembly / positive regulation of protein localization to presynapse / skeletal muscle satellite cell activation / regulation of axon diameter / asymmetric protein localization involved in cell fate determination / lens fiber cell development / cerebellar granule cell differentiation / WNT ligand biogenesis and trafficking / oviduct development / synaptic vesicle recycling / central nervous system vasculogenesis / cell proliferation in forebrain / excitatory synapse assembly / uterus morphogenesis / embryonic axis specification / secondary palate development / presynapse assembly / somatic stem cell division / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / stem cell development / sex differentiation / protein-containing complex destabilizing activity / [Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / positive regulation of epithelial cell proliferation involved in wound healing / phospholipase C activity / Release of Hh-Np from the secreting cell / regulation of bone mineralization / establishment of blood-brain barrier / dendritic spine morphogenesis / frizzled binding / dorsal/ventral pattern formation / neurotransmitter secretion / embryonic forelimb morphogenesis / Class B/2 (Secretin family receptors) / regulation of postsynapse organization / embryonic hindlimb morphogenesis / positive regulation of synapse assembly / wound healing, spreading of epidermal cells / Wnt signaling pathway, planar cell polarity pathway / embryonic digit morphogenesis / cartilage condensation / establishment of cell polarity / regulation of synaptic vesicle exocytosis / negative regulation of Wnt signaling pathway / positive regulation of protein metabolic process / somatic stem cell population maintenance / cell fate commitment / positive regulation of excitatory postsynaptic potential / chondrocyte differentiation / canonical Wnt signaling pathway / regulation of presynapse assembly / cellular response to transforming growth factor beta stimulus / extracellular matrix / positive regulation of endothelial cell migration / axonogenesis / cytokine activity / positive regulation of JNK cascade / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway / bone development / negative regulation of neurogenesis / Golgi lumen / response to estrogen / Schaffer collateral - CA1 synapse / Wnt signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron differentiation / endocytic vesicle membrane / response to estradiol / presynapse / angiogenesis / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / apoptotic process / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / glutamatergic synapse / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Wnt-7 protein / Wnt protein, conserved site / Wnt-1 family signature. / Wnt / Wnt, C-terminal domain / wnt family / found in Wnt-1 / Pectinacetylesterase/NOTUM / Pectinacetylesterase
Similarity search - Domain/homology
PALMITOLEIC ACID / Protein Wnt-7a / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.5 Å
AuthorsZebisch, M. / Jones, E.Y.
CitationJournal: Nature / Year: 2015
Title: Notum Deacylates Wnt Proteins to Suppress Signalling Activity.
Authors: Kakugawa, S. / Langton, P.F. / Zebisch, M. / Howell, S.A. / Chang, T. / Liu, Y. / Feizi, T. / Bineva, G. / O'Reilly, N. / Snijders, A.P. / Jones, E.Y. / Vincent, J.
History
DepositionSep 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Structure summary
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Jul 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 / pdbx_struct_conn_angle / 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 / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: PROTEIN NOTUM HOMOLOG
B: PROTEIN WNT-7A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3529
Polymers44,7242
Non-polymers6287
Water5,495305
1
A: PROTEIN NOTUM HOMOLOG
B: PROTEIN WNT-7A
hetero molecules

A: PROTEIN NOTUM HOMOLOG
B: PROTEIN WNT-7A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,70518
Polymers89,4494
Non-polymers1,25614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4440 Å2
ΔGint-90.6 kcal/mol
Surface area29530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.513, 69.350, 120.967
Angle α, β, γ (deg.)90.00, 92.28, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-2146-

HOH

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Components

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

#1: Protein PROTEIN NOTUM HOMOLOG / NOTUM


Mass: 43974.547 Da / Num. of mol.: 1 / Fragment: RESIDUES 81-451 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: GLYCOSYLATED AT N96 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q6P988, carboxylesterase
#2: Protein/peptide PROTEIN WNT-7A


Mass: 749.838 Da / Num. of mol.: 1 / Fragment: RESIDUES 202-209 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O00755
#3: 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.: 1
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 , 4 types, 311 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsGAMMA-PALMITOLEOYL-SERINE: WNT FRAGMENT ESTER BETWEEN SERINE OF WNT FRAGMENT AND PALMITOLEIC ACID
Sequence detailsC330S ENGINEERED MUTATION S232A INACTIVE MUTANT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 5 / Details: 3.0M NACL, 0.1 M CITRATE PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.00,1.07
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.071
ReflectionResolution: 1.5→60 Å / Num. obs: 64352 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.5→60.44 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.98 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17775 1255 2 %RANDOM
Rwork0.12789 ---
obs0.12888 62998 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.448 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å2-0.46 Å2
2--0.67 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.5→60.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 36 305 3190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193056
X-RAY DIFFRACTIONr_bond_other_d0.0010.022869
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.954163
X-RAY DIFFRACTIONr_angle_other_deg0.94436578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0675377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77421.933150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22115500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3591537
X-RAY DIFFRACTIONr_chiral_restr0.1270.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213462
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02777
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_it2.8281.2061445
X-RAY DIFFRACTIONr_mcbond_other2.8121.21444
X-RAY DIFFRACTIONr_mcangle_it3.1941.8141807
X-RAY DIFFRACTIONr_mcangle_other3.2051.821808
X-RAY DIFFRACTIONr_scbond_it6.6081.8991611
X-RAY DIFFRACTIONr_scbond_other6.6061.9011612
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5822.6122345
X-RAY DIFFRACTIONr_long_range_B_refined6.32111.9393745
X-RAY DIFFRACTIONr_long_range_B_other6.3211.9493746
X-RAY DIFFRACTIONr_rigid_bond_restr4.38735925
X-RAY DIFFRACTIONr_sphericity_free38.7275134
X-RAY DIFFRACTIONr_sphericity_bonded18.01256008
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 77 -
Rwork0.241 4294 -
obs--88.93 %

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