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- PDB-6qgq: Crystal structure of APT1 C2S mutant bound to palmitic acid. -

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Basic information

Entry
Database: PDB / ID: 6qgq
TitleCrystal structure of APT1 C2S mutant bound to palmitic acid.
Components(Acyl-protein thioesterase 1) x 2
KeywordsHYDROLASE / acyl-protein thioesterase / palmitic acid / Depalmitoylation
Function / homology
Function and homology information


protein depalmitoylation / negative regulation of Golgi to plasma membrane protein transport / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / negative regulation of aggrephagy / glycerophospholipase activity / lipase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / carboxylic ester hydrolase activity / phosphatidylcholine lysophospholipase A1 activity ...protein depalmitoylation / negative regulation of Golgi to plasma membrane protein transport / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / negative regulation of aggrephagy / glycerophospholipase activity / lipase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / carboxylic ester hydrolase activity / phosphatidylcholine lysophospholipase A1 activity / fatty acid transport / eNOS activation / fatty acid metabolic process / RAS processing / nuclear membrane / endoplasmic reticulum / mitochondrion / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / Acyl-protein thioesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsAudagnotto, M. / Marcaida, M.J. / Ho, S. / Pojer, F. / Van der Goot, G. / Dal Peraro, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation200020_157153 Switzerland
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Palmitoylated acyl protein thioesterase APT2 deforms membranes to extract substrate acyl chains.
Authors: Abrami, L. / Audagnotto, M. / Ho, S. / Marcaida, M.J. / Mesquita, F.S. / Anwar, M.U. / Sandoz, P.A. / Fonti, G. / Pojer, F. / Dal Peraro, M. / van der Goot, F.G.
History
DepositionJan 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 31, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-protein thioesterase 1
B: Acyl-protein thioesterase 1
C: Acyl-protein thioesterase 1
D: Acyl-protein thioesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,86410
Polymers99,9824
Non-polymers8816
Water2,378132
1
A: Acyl-protein thioesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1623
Polymers24,9781
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acyl-protein thioesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3052
Polymers25,0491
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acyl-protein thioesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0702
Polymers24,9781
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Acyl-protein thioesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3263
Polymers24,9781
Non-polymers3492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.138, 160.738, 40.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Acyl-protein thioesterase 1 / hAPT1 / Lysophospholipase 1 / Lysophospholipase I / LysoPLA I


Mass: 24977.805 Da / Num. of mol.: 3 / Mutation: C2S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYPLA1, APT1, LPL1 / Production host: Escherichia coli (E. coli)
References: UniProt: O75608, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Protein Acyl-protein thioesterase 1 / hAPT1 / Lysophospholipase 1 / Lysophospholipase I / LysoPLA I


Mass: 25048.883 Da / Num. of mol.: 1 / Mutation: C2S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYPLA1, APT1, LPL1 / Production host: Escherichia coli (E. coli)
References: UniProt: O75608, Hydrolases; Acting on ester bonds; Thioester hydrolases
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C16H32O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 25% of of polyethylene glycol (PEG) 2000 MME, 0.3 M sodium acetate, 0.1 M sodium cacodylate pH 6.5;

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.71 Å / Num. obs: 30525 / % possible obs: 99.9 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.6
Reflection shellResolution: 2.6→2.74 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FJ2

1fj2


Resolution: 2.601→46.619 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.47
RfactorNum. reflection% reflection
Rfree0.238 1481 4.86 %
Rwork0.1909 --
obs0.1932 30461 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.601→46.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6680 0 53 132 6865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036883
X-RAY DIFFRACTIONf_angle_d0.5419343
X-RAY DIFFRACTIONf_dihedral_angle_d6.8184162
X-RAY DIFFRACTIONf_chiral_restr0.0421065
X-RAY DIFFRACTIONf_plane_restr0.0041205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6015-2.68540.24321290.22582591X-RAY DIFFRACTION99
2.6854-2.78140.31041170.23032572X-RAY DIFFRACTION100
2.7814-2.89270.29941490.22952614X-RAY DIFFRACTION100
2.8927-3.02440.28941480.23132534X-RAY DIFFRACTION100
3.0244-3.18380.28241280.22052608X-RAY DIFFRACTION100
3.1838-3.38320.24291180.20572651X-RAY DIFFRACTION100
3.3832-3.64430.22671630.18532565X-RAY DIFFRACTION100
3.6443-4.01090.21841210.17622653X-RAY DIFFRACTION100
4.0109-4.59080.1811290.15512673X-RAY DIFFRACTION100
4.5908-5.78220.23381460.17192683X-RAY DIFFRACTION100
5.7822-46.62630.22631330.18842836X-RAY DIFFRACTION100

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