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- PDB-8ayf: Crystal structure of human Sphingosine-1-phosphate lyase 1 -

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Basic information

Entry
Database: PDB / ID: 8ayf
TitleCrystal structure of human Sphingosine-1-phosphate lyase 1
ComponentsSphingosine-1-phosphate lyase 1
KeywordsLYASE / S1P / lipid
Function / homology
Function and homology information


sphinganine-1-phosphate aldolase / Sphingolipid catabolism / sphinganine-1-phosphate aldolase activity / luteinization / ceramide metabolic process / Leydig cell differentiation / fibroblast migration / sphingolipid catabolic process / estrogen metabolic process / face morphogenesis ...sphinganine-1-phosphate aldolase / Sphingolipid catabolism / sphinganine-1-phosphate aldolase activity / luteinization / ceramide metabolic process / Leydig cell differentiation / fibroblast migration / sphingolipid catabolic process / estrogen metabolic process / face morphogenesis / skeletal system morphogenesis / platelet-derived growth factor receptor signaling pathway / roof of mouth development / hemopoiesis / androgen metabolic process / regulation of multicellular organism growth / vasculogenesis / post-embryonic development / apoptotic signaling pathway / kidney development / fatty acid metabolic process / pyridoxal phosphate binding / spermatogenesis / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
: / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
ACETATE ION / Sphingosine-1-phosphate lyase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsGiardina, G. / Catalano, F. / Pampalone, G. / Cellini, B.
Funding support Italy, 3items
OrganizationGrant numberCountry
Other governmentRP11916B407928AA Italy
Other governmentRM12117A5BDD4AEC Italy
Other privateFFC#16/2020 Italy
CitationJournal: Sci Rep / Year: 2023
Title: Dual species sphingosine-1-phosphate lyase inhibitors to combine antifungal and anti-inflammatory activities in cystic fibrosis: a feasibility study.
Authors: Cellini, B. / Pampalone, G. / Camaioni, E. / Pariano, M. / Catalano, F. / Zelante, T. / Dindo, M. / Macchioni, L. / Di Veroli, A. / Galarini, R. / Paoletti, F. / Davidescu, M. / Stincardini, ...Authors: Cellini, B. / Pampalone, G. / Camaioni, E. / Pariano, M. / Catalano, F. / Zelante, T. / Dindo, M. / Macchioni, L. / Di Veroli, A. / Galarini, R. / Paoletti, F. / Davidescu, M. / Stincardini, C. / Vascelli, G. / Bellet, M.M. / Saba, J. / Giovagnoli, S. / Giardina, G. / Romani, L. / Costantini, C.
History
DepositionSep 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Jan 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sphingosine-1-phosphate lyase 1
B: Sphingosine-1-phosphate lyase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2996
Polymers109,9972
Non-polymers3024
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14490 Å2
ΔGint-102 kcal/mol
Surface area30870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.160, 127.410, 66.950
Angle α, β, γ (deg.)90.000, 104.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sphingosine-1-phosphate lyase 1 / S1PL / SP-lyase 1 / SPL 1 / hSPL / Sphingosine-1-phosphate aldolase


Mass: 54998.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Expressed as a deletion mutant of the first 81 residues - Delta81
Source: (gene. exp.) Homo sapiens (human) / Gene: SGPL1, KIAA1252 / Plasmid: pET28-b
Details (production host): co transformed with pGRO7 plasmid from Takara containing GroEL and GroES chaperonins
Production host: Escherichia coli BL21 (bacteria)
References: UniProt: O95470, sphinganine-1-phosphate aldolase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.97 Å3/Da / Density % sol: 37.63 % / Description: Platelets
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein solution: hSPL 108uM in Tris-HCl 20 mM pH 8.0 NaCl 150 mM DTT 1mM Glycerol 5% Precipitant: (Hit G4 of Molecular Dimension screen Morpheus) 0.02M Sodium formate; 0.02M Ammonium ...Details: Protein solution: hSPL 108uM in Tris-HCl 20 mM pH 8.0 NaCl 150 mM DTT 1mM Glycerol 5% Precipitant: (Hit G4 of Molecular Dimension screen Morpheus) 0.02M Sodium formate; 0.02M Ammonium acetate; 0.02M Sodium citrate tribasic dihydrate; 0.02M Potassium sodium tartrate tetrahydrate; 0.02M Sodium oxamate; Imidazole 0.05M; MES monohydrate (acid) 0.05M; 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350 mixing volumes: 0.3 + 0.3 uL

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2022
Details: Cilindrical Mirror with 50 nm Pt-coating Radius (calculated) = 14 km Distance from source = 21200 mm Incidence angle = 3 mrad Active length = 1200 mm
RadiationMonochromator: Double Crystal Si111 with LN2 closed loop cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→57.76 Å / Num. obs: 47604 / % possible obs: 92.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 18.8 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.8
Reflection shellResolution: 1.84→2.09 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2380 / CC1/2: 0.421 / % possible all: 67.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.532
Highest resolutionLowest resolution
Rotation57.7 Å2.31 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q6R

4q6r


Resolution: 1.84→57.76 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.1816 / WRfactor Rwork: 0.16 / FOM work R set: 0.8278 / SU B: 4.289 / SU ML: 0.121 / SU R Cruickshank DPI: 0.2877 / SU Rfree: 0.1937 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.288 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 2499 5.2 %RANDOM
Rwork0.1907 ---
obs0.192 45105 57.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.44 Å2 / Biso mean: 21.609 Å2 / Biso min: 8.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 1.84→57.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6858 0 28 319 7205
Biso mean--23.87 27.82 -
Num. residues----891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127079
X-RAY DIFFRACTIONr_bond_other_d0.0110.0166472
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.6429599
X-RAY DIFFRACTIONr_angle_other_deg0.5181.55615042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.445896
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.549536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.486101125
X-RAY DIFFRACTIONr_chiral_restr0.0660.21064
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021439
LS refinement shellResolution: 1.84→1.886 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.421 5 -
Rwork0.282 149 -
obs--2.52 %

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