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- PDB-6qgn: Crystal structure of APT1 bound to 2-Bromopalmitate -

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Basic information

Entry
Database: PDB / ID: 6qgn
TitleCrystal structure of APT1 bound to 2-Bromopalmitate
ComponentsAcyl-protein thioesterase 1
KeywordsHYDROLASE / acyl-protein thioesterase 2-bromopalmitate 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 / phospholipase activity / lipase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / carboxylic ester hydrolase activity / lysophospholipase activity ...protein depalmitoylation / negative regulation of Golgi to plasma membrane protein transport / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / negative regulation of aggrephagy / phospholipase activity / lipase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / carboxylic ester hydrolase activity / lysophospholipase 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
2-Bromopalmitic acid / Acyl-protein thioesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsMarcaida, M.J. / Audagnotto, M. / 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)101,2538
Polymers99,9114
Non-polymers1,3414
Water7,891438
1
A: Acyl-protein thioesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3132
Polymers24,9781
Non-polymers3351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acyl-protein thioesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3132
Polymers24,9781
Non-polymers3351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acyl-protein thioesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3132
Polymers24,9781
Non-polymers3351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Acyl-protein thioesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3132
Polymers24,9781
Non-polymers3351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.900, 109.616, 174.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 4 / 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: Chemical
ChemComp-J1W / 2-Bromopalmitic acid


Mass: 335.320 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H31BrO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: D1 Morpheus (Molecular Dimensions) 0.1 M imidazole, 0.1 M MES monohydrate, 20% v/v PEG 500 MME, 10% w/v PEG 2000, 20 mM 1,6-Hexanediol, 20 mM 1-Butanol, 20 mM 1,2-Propanediol, 20 mM 2- ...Details: D1 Morpheus (Molecular Dimensions) 0.1 M imidazole, 0.1 M MES monohydrate, 20% v/v PEG 500 MME, 10% w/v PEG 2000, 20 mM 1,6-Hexanediol, 20 mM 1-Butanol, 20 mM 1,2-Propanediol, 20 mM 2- Propanol, 20 mM 1,4-Butanediol, 20 mM 1,3-Propanediol, 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: 0.91971 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91971 Å / Relative weight: 1
ReflectionResolution: 2.09→46.427 Å / Num. obs: 66902 / % possible obs: 99.5 % / Redundancy: 7.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.8
Reflection shellResolution: 2.09→2.21 Å / Redundancy: 7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 9483 / CC1/2: 0.71 / % possible all: 98.3

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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: 5SYM

5sym


Resolution: 2.099→46.427 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.17
RfactorNum. reflection% reflection
Rfree0.2733 3446 5.16 %
Rwork0.23 --
obs0.2322 66823 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.099→46.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6712 0 76 438 7226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076962
X-RAY DIFFRACTIONf_angle_d0.839453
X-RAY DIFFRACTIONf_dihedral_angle_d7.6845014
X-RAY DIFFRACTIONf_chiral_restr0.0491078
X-RAY DIFFRACTIONf_plane_restr0.0061222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0992-2.12790.32791520.27512327X-RAY DIFFRACTION94
2.1279-2.15830.29961320.24552504X-RAY DIFFRACTION100
2.1583-2.19060.30181600.24322509X-RAY DIFFRACTION100
2.1906-2.22480.3191150.24692504X-RAY DIFFRACTION100
2.2248-2.26130.3361180.24432565X-RAY DIFFRACTION100
2.2613-2.30030.331440.23512462X-RAY DIFFRACTION100
2.3003-2.34210.26551310.2322529X-RAY DIFFRACTION100
2.3421-2.38710.2841250.2232516X-RAY DIFFRACTION100
2.3871-2.43580.32611400.23512518X-RAY DIFFRACTION100
2.4358-2.48880.28411420.2382507X-RAY DIFFRACTION100
2.4888-2.54670.30931390.24132523X-RAY DIFFRACTION100
2.5467-2.61040.3081220.23862537X-RAY DIFFRACTION100
2.6104-2.6810.3121220.24232542X-RAY DIFFRACTION100
2.681-2.75980.26111410.23242494X-RAY DIFFRACTION100
2.7598-2.84890.30031400.23572528X-RAY DIFFRACTION100
2.8489-2.95070.32151520.24342542X-RAY DIFFRACTION100
2.9507-3.06880.27481220.24432535X-RAY DIFFRACTION100
3.0688-3.20850.29381510.2482529X-RAY DIFFRACTION100
3.2085-3.37760.31121100.24072569X-RAY DIFFRACTION100
3.3776-3.58910.26081570.23512535X-RAY DIFFRACTION100
3.5891-3.86610.27141280.22952577X-RAY DIFFRACTION100
3.8661-4.25490.25491360.21692585X-RAY DIFFRACTION100
4.2549-4.87010.21351420.19972594X-RAY DIFFRACTION100
4.8701-6.13350.25851590.22112609X-RAY DIFFRACTION100
6.1335-46.43820.2211660.21052737X-RAY DIFFRACTION100

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