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- PDB-3dww: Electron crystallographic structure of human microsomal prostagla... -

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Basic information

Entry
Database: PDB / ID: 3dww
TitleElectron crystallographic structure of human microsomal prostaglandin E synthase 1
ComponentsProstaglandin E synthase
KeywordsISOMERASE / membrane protein / four helix bundle / Membrane / Transmembrane
Function / homology
Function and homology information


regulation of fever generation / prostaglandin-E synthase / prostaglandin-E synthase activity / prostaglandin-D synthase activity / positive regulation of prostaglandin secretion / glutathione binding / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / glutathione peroxidase activity / prostaglandin biosynthetic process / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases ...regulation of fever generation / prostaglandin-E synthase / prostaglandin-E synthase activity / prostaglandin-D synthase activity / positive regulation of prostaglandin secretion / glutathione binding / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / glutathione peroxidase activity / prostaglandin biosynthetic process / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / prostaglandin metabolic process / nuclear envelope lumen / glutathione transferase / glutathione transferase activity / sensory perception of pain / regulation of inflammatory response / cell population proliferation / negative regulation of cell population proliferation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / signal transduction / membrane
Similarity search - Function
Microsomal glutathione S-transferase 1-like / Membrane associated eicosanoid/glutathione metabolism-like domain / Membrane-associated, eicosanoid/glutathione metabolism (MAPEG) protein / Membrane associated eicosanoid/glutathione metabolism-like domain superfamily / MAPEG family / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
GLUTATHIONE / Prostaglandin E synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 3.5 Å
AuthorsHebert, H. / Jegerschold, C.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2008
Title: Structural basis for induced formation of the inflammatory mediator prostaglandin E2.
Authors: Caroline Jegerschöld / Sven-Christian Pawelzik / Pasi Purhonen / Priyaranjan Bhakat / Karina Roxana Gheorghe / Nobuhiko Gyobu / Kaoru Mitsuoka / Ralf Morgenstern / Per-Johan Jakobsson / Hans Hebert /
Abstract: Prostaglandins (PG) are bioactive lipids produced from arachidonic acid via the action of cyclooxygenases and terminal PG synthases. Microsomal prostaglandin E synthase 1 (MPGES1) constitutes an ...Prostaglandins (PG) are bioactive lipids produced from arachidonic acid via the action of cyclooxygenases and terminal PG synthases. Microsomal prostaglandin E synthase 1 (MPGES1) constitutes an inducible glutathione-dependent integral membrane protein that catalyzes the oxidoreduction of cyclooxygenase derived PGH(2) into PGE(2). MPGES1 has been implicated in a number of human diseases or pathological conditions, such as rheumatoid arthritis, fever, and pain, and is therefore regarded as a primary target for development of novel antiinflammatory drugs. To provide a structural basis for insight in the catalytic mechanism, we determined the structure of MPGES1 in complex with glutathione by electron crystallography from 2D crystals induced in the presence of phospholipids. Together with results from site-directed mutagenesis and activity measurements, we can thereby demonstrate the role of specific amino acid residues. Glutathione is found to bind in a U-shaped conformation at the interface between subunits in the protein trimer. It is exposed to a site facing the lipid bilayer, which forms the specific environment for the oxidoreduction of PGH(2) to PGE(2) after displacement of the cytoplasmic half of the N-terminal transmembrane helix. Hence, insight into the dynamic behavior of MPGES1 and homologous membrane proteins in inflammation and detoxification is provided.
History
DepositionJul 23, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Non-polymer description
Revision 1.3Mar 20, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / em_single_particle_entity / em_vitrification / struct_ref_seq_dif / struct_site
Item: _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id ..._struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Assembly

Deposited unit
A: Prostaglandin E synthase
B: Prostaglandin E synthase
C: Prostaglandin E synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7796
Polymers53,8573
Non-polymers9223
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.200, 84.600, 100.000
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 Prostaglandin E synthase / / Microsomal prostaglandin E synthase 1 / Microsomal glutathione S-transferase 1-like 1 / MGST1-L1 / ...Microsomal prostaglandin E synthase 1 / Microsomal glutathione S-transferase 1-like 1 / MGST1-L1 / p53-induced gene 12 protein


Mass: 17952.205 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSP19T7LT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star(DE) / References: UniProt: O14684, prostaglandin-E synthase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N3O6S

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: human microsomal prostaglandin E synthase 1 / Type: COMPLEX
Details: Embedded in trehalose and frozen in liquid nitrogen
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingDetails: 3 % trehalose / Material: trehalose

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Data collection

MicroscopyModel: JEOL 2100F / Details: Electron diffraction patterns
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Specimen holderTemperature: 100 K / Tilt angle max: 60 °
Image recordingFilm or detector model: TVIPS TEMCAM-F415 (4k x 4k)

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Processing

3D reconstructionResolution: 3.5 Å
Details: Phase information obtained by molecular replacement using the structure of microsomal glutathione transferase 1
Symmetry type: 2D CRYSTAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 0 60 0 3456

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