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- PDB-8hta: Solution Structure of the C65A/C167A Mutant of Human Lipocalin-ty... -

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Basic information

Entry
Database: PDB / ID: 8hta
TitleSolution Structure of the C65A/C167A Mutant of Human Lipocalin-type Prostaglandin D Synthase
ComponentsProstaglandin-H2 D-isomerase
KeywordsISOMERASE / LIPOCALIN / BETA-BARREL / FATTY ACID BIOSYNTHESIS / GLYCOPROTEIN / PROSTAGLANDIN BIOSYNTHESIS / SECRETED / TRANSPORT
Function / homology
Function and homology information


prostaglandin-D synthase / prostaglandin-D synthase activity / Transcriptional regulation of testis differentiation / negative regulation of male germ cell proliferation / regulation of circadian sleep/wake cycle, sleep / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / cyclooxygenase pathway / retinoid binding / prostaglandin biosynthetic process / mast cell degranulation ...prostaglandin-D synthase / prostaglandin-D synthase activity / Transcriptional regulation of testis differentiation / negative regulation of male germ cell proliferation / regulation of circadian sleep/wake cycle, sleep / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / cyclooxygenase pathway / retinoid binding / prostaglandin biosynthetic process / mast cell degranulation / response to glucocorticoid / rough endoplasmic reticulum / fatty acid binding / gene expression / nuclear membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin signature.
Similarity search - Domain/homology
Prostaglandin-H2 D-isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMiyamoto, Y. / Inui, T.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25242046 Japan
Japan Society for the Promotion of Science (JSPS)17300165 Japan
Japan Society for the Promotion of Science (JSPS)21500428 Japan
Japan Society for the Promotion of Science (JSPS)21200076 Japan
Japan Society for the Promotion of Science (JSPS)09J10176 Japan
CitationJournal: Febs J. / Year: 2023
Title: Structural and interaction analysis of human lipocalin-type prostaglandin D synthase with the poorly water-soluble drug NBQX.
Authors: Miyamoto, Y. / Nakatsuji, M. / Yoshida, T. / Ohkubo, T. / Inui, T.
History
DepositionDec 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prostaglandin-H2 D-isomerase


Theoretical massNumber of molelcules
Total (without water)18,7971
Polymers18,7971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11570 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 5000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Prostaglandin-H2 D-isomerase / Beta-trace protein / Cerebrin-28 / Glutathione-independent PGD synthase / Lipocalin-type ...Beta-trace protein / Cerebrin-28 / Glutathione-independent PGD synthase / Lipocalin-type prostaglandin-D synthase / L-PGDS / Prostaglandin-D2 synthase / PGD2 synthase / PGDS / PGDS2


Mass: 18796.988 Da / Num. of mol.: 1 / Mutation: C65A,C167A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTGDS, PDS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41222, prostaglandin-D synthase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D 1H-15N NOESY
151isotropic13D 1H-15N TOCSY
262isotropic12D 13C-1H (HB)CB(CGCD)HD
2122isotropic13D (H)CCH-TOCSY
2112isotropic13D 1H-13C NOESY aliphatic
2102isotropic13D 1H-13C NOESY aromatic
2132isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution120 mM [U-2H] acetic acid, 500 mM [U-13C; U-15N] Prostaglandin-H2 D-isomerase, 10 % [U-99% 2H] D2O, 90% H2O/10% D2O15N/13C_sample_H2O90% H2O/10% D2O
solution220 mM [U-2H] acetic acid, 500 mM [U-13C; U-15N] Prostaglandin-H2 D-isomerase, 99.95 % [U-100% 2H] D2O, 99.95% D2O15N/13C_sample_D2O99.95% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMacetic acid[U-2H]1
500 mMProstaglandin-H2 D-isomerase[U-13C; U-15N]1
10 %D2O[U-99% 2H]1
20 mMacetic acid[U-2H]2
500 mMProstaglandin-H2 D-isomerase[U-13C; U-15N]2
99.95 %D2O[U-100% 2H]2
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
10.5 mM [U-13C; U-15N] Prostaglandin-H2 D-isomerase, 20 mM [U-2H] acetic acid, 90% H2O/10% D2O20 mMconditions_H2O41 atm308 K
20.5 mM [U-13C; U-15N] Prostaglandin-H2 D-isomerase, 20 mM [U-2H] acetic acid, 99.95% D2O20 mMconditions_D2O41 atm308 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
Sparky3.115Goddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 5000 / Conformers submitted total number: 10

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