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- PDB-7kze: Substrate-dependent divergence of leukotriene A4 hydrolase aminop... -

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Basic information

Entry
Database: PDB / ID: 7kze
TitleSubstrate-dependent divergence of leukotriene A4 hydrolase aminopeptidase activity
ComponentsLeukotriene A-4 hydrolase
KeywordsHYDROLASE / Leukotriene A4 hydrolase / 4MDM / Aminipeptidase / Activator
Function / homology
Function and homology information


leukotriene-A4 hydrolase / tripeptide aminopeptidase / tripeptide aminopeptidase activity / leukotriene-A4 hydrolase activity / Biosynthesis of protectins / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Synthesis of Leukotrienes (LT) and Eoxins (EX) ...leukotriene-A4 hydrolase / tripeptide aminopeptidase / tripeptide aminopeptidase activity / leukotriene-A4 hydrolase activity / Biosynthesis of protectins / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Synthesis of Leukotrienes (LT) and Eoxins (EX) / protein metabolic process / leukotriene biosynthetic process / epoxide hydrolase activity / type I pneumocyte differentiation / peptide catabolic process / response to zinc ion / metalloaminopeptidase activity / aminopeptidase activity / lipid metabolic process / response to peptide hormone / tertiary granule lumen / peptidase activity / ficolin-1-rich granule lumen / Neutrophil degranulation / proteolysis / RNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
Leukotriene A4 hydrolase/leucine aminopeptidase / Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain ...Leukotriene A4 hydrolase/leucine aminopeptidase / Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Armadillo-type fold
Similarity search - Domain/homology
1-benzyl-4-methoxybenzene / TRIETHYLENE GLYCOL / Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLee, K.H. / Shim, Y. / Paige, M. / Noble, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL132287 United States
CitationJournal: Sci Rep / Year: 2022
Title: Substrate-dependent modulation of the leukotriene A 4 hydrolase aminopeptidase activity and effect in a murine model of acute lung inflammation.
Authors: Lee, K.H. / Ali, N.F. / Lee, S.H. / Zhang, Z. / Burdick, M. / Beaulac, Z.J. / Petruncio, G. / Li, L. / Xiang, J. / Chung, E.M. / Foreman, K.W. / Noble, S.M. / Shim, Y.M. / Paige, M.
History
DepositionDec 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: 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
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leukotriene A-4 hydrolase
B: Leukotriene A-4 hydrolase
C: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,7639
Polymers207,0203
Non-polymers7436
Water11,187621
1
A: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2703
Polymers69,0071
Non-polymers2642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2223
Polymers69,0071
Non-polymers2162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2703
Polymers69,0071
Non-polymers2642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)139.888, 139.888, 84.343
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Leukotriene A-4 hydrolase / LTA-4 hydrolase / Leukotriene A(4) hydrolase


Mass: 69006.547 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTA4H, LTA4 / Production host: Escherichia coli (E. coli)
References: UniProt: P09960, leukotriene-A4 hydrolase, tripeptide aminopeptidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-N0Y / 1-benzyl-4-methoxybenzene


Mass: 198.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 60-75 mM magnesium formate dihydrate, 19-23 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→53.84 Å / Num. obs: 80258 / % possible obs: 98.02 % / Redundancy: 9.75 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.41
Reflection shellResolution: 2.9→3.004 Å / Rmerge(I) obs: 0.3198 / Num. unique obs: 40210

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
PROTEUMdata reduction
PROTEUMdata scaling
PROTEUMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MS6

4ms6


Resolution: 2.9→53.84 Å / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 22.24 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2088 3976 4.95 %
Rwork0.1945 --
obs0.1922 80258 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→53.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14572 0 43 621 15236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215033
X-RAY DIFFRACTIONf_angle_d0.63520439
X-RAY DIFFRACTIONf_dihedral_angle_d10.9635548
X-RAY DIFFRACTIONf_chiral_restr0.0252280
X-RAY DIFFRACTIONf_plane_restr0.0032602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9006-2.95060.28381760.2613379X-RAY DIFFRACTION81
2.9506-3.00410.34251860.25113420X-RAY DIFFRACTION84
3.0041-3.06180.29751620.24773568X-RAY DIFFRACTION88
3.0618-3.12420.26431980.22473746X-RAY DIFFRACTION91
3.1242-3.1920.24722020.22063795X-RAY DIFFRACTION94
3.192-3.26610.27192040.20873964X-RAY DIFFRACTION95
3.2661-3.34760.23242040.21133824X-RAY DIFFRACTION95
3.3476-3.43780.23951900.20613896X-RAY DIFFRACTION95
3.4378-3.53870.23172000.19813886X-RAY DIFFRACTION95
3.5387-3.65260.22341920.20063957X-RAY DIFFRACTION95
3.6526-3.78270.24151960.19223851X-RAY DIFFRACTION95
3.7827-3.93350.22761990.17933849X-RAY DIFFRACTION95
3.9335-4.11180.18152120.17583900X-RAY DIFFRACTION95
4.1118-4.32750.16882040.16933854X-RAY DIFFRACTION95
4.3275-4.5970.18042000.16283860X-RAY DIFFRACTION95
4.597-4.94920.15641840.15573960X-RAY DIFFRACTION96
4.9492-5.44240.20221960.16823872X-RAY DIFFRACTION95
5.4424-6.21880.21461960.18523858X-RAY DIFFRACTION95
6.2188-7.79350.1882160.17553904X-RAY DIFFRACTION95
7.7935-24.60080.14842000.15683858X-RAY DIFFRACTION95

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