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- PDB-3b7s: [E296Q]LTA4H in complex with RSR substrate -

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Basic information

Entry
Database: PDB / ID: 3b7s
Title[E296Q]LTA4H in complex with RSR substrate
Components
  • Leukotriene A-4 hydrolase
  • RSR peptide
KeywordsHYDROLASE / TRANSITION STATE / ANALOGUE PEPTIDE / HYDROLYSIS / LEUKOTRIENE BIOSYNTHESIS / METAL-BINDING / METALLOPROTEASE / MULTIFUNCTIONAL ENZYME / PROTEASE / TRIPEPTIDE SUBSTRATE
Function / homology
Function and homology information


leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase activity / tripeptide aminopeptidase / Biosynthesis of protectins / protein metabolic process / 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 ...leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase activity / tripeptide aminopeptidase / Biosynthesis of protectins / protein metabolic process / 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) / epoxide hydrolase activity / leukotriene biosynthetic process / response to zinc ion / peptide catabolic process / type I pneumocyte differentiation / metalloaminopeptidase activity / aminopeptidase activity / response to peptide hormone / lipid metabolic process / tertiary granule lumen / peptidase activity / ficolin-1-rich granule lumen / Neutrophil degranulation / proteolysis / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal domain / Leukotriene A4 hydrolase/leucine aminopeptidase / Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / : / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / Zincin-like - #30 / Zincin-like ...Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal domain / Leukotriene A4 hydrolase/leucine aminopeptidase / Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / : / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / Zincin-like - #30 / Zincin-like / tricorn interacting facor f3 domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / YTTERBIUM (III) ION / Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.465 Å
AuthorsTholander, F. / Haeggstrom, J. / Thunnissen, M. / Muroya, A. / Roques, B.-P. / Fournie-Zaluski, M.-C.
Citation
Journal: Chem.Biol. / Year: 2008
Title: Structure-based dissection of the active site chemistry of leukotriene a4 hydrolase: implications for m1 aminopeptidases and inhibitor design.
Authors: Tholander, F. / Muroya, A. / Roques, B.P. / Fournie-Zaluski, M.C. / Thunnissen, M.M. / Haeggstrom, J.Z.
#1: Journal: Proteins / Year: 2007
Title: Assay for rapid analysis of the tri-peptidase activity of LTA4 hydrolase.
Authors: Tholander, F. / Haeggstrom, J.Z.
#2: Journal: J.Biol.Chem. / Year: 2004
Title: Leukotriene A4 hydrolase: identification of a common carboxylate recognition site for the epoxide hydrolase and aminopeptidase substrates.
Authors: Rudberg, P.C. / Tholander, F. / Andberg, M. / Thunnissen, M.M. / Haeggstrom, J.Z.
#3: Journal: J.Biol.Chem. / Year: 2002
Title: Leukotriene A4 hydrolase/aminopeptidase. Glutamate 271 is a catalytic residue with specific roles in two distinct enzyme mechanisms.
Authors: Rudberg, P.C. / Tholander, F. / Thunnissen, M.M. / Haeggstrom, J.Z.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Leukotriene A4 hydrolase: selective abrogation of leukotriene B4 formation by mutation of aspartic acid 375.
Authors: Rudberg, P.C. / Tholander, F. / Thunnissen, M.M. / Samuelsson, B. / Haeggstrom, J.Z.
#5: Journal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of human leukotriene A(4) hydrolase, a bifunctional enzyme in inflammation.
Authors: Thunnissen, M.M. / Nordlund, P. / Haeggstrom, J.Z.
History
DepositionOct 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 7, 2018Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Oct 20, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Leukotriene A-4 hydrolase
B: RSR peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8716
Polymers70,4802
Non-polymers3914
Water10,899605
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.508, 87.351, 99.769
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Leukotriene A-4 hydrolase / LTA-4 hydrolase / Leukotriene A(4) hydrolase / Tripeptide aminopeptidase LTA4H


Mass: 70060.664 Da / Num. of mol.: 1 / Mutation: E296Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTA4H, LTA4 / Plasmid: pT7T3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101
References: UniProt: P09960, leukotriene-A4 hydrolase, tripeptide aminopeptidase
#2: Protein/peptide RSR peptide


Mass: 419.481 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 5 types, 609 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Yb
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 298 K / Method: liquid-liquid diffusion
Details: TRI-PEPTIDE WAS CO-CRYSTALLIZED WITH [E296Q]LTA4H BY LIQUID-LIQUID DIFFUSION IN MELTING-POINT CAPILLARIES. A TRIS-BUFFERED (10 mM, PH 7.5) SOLUTION OF PROTEIN AND TRIPEPTIDE, MOLAR RATIO 1: ...Details: TRI-PEPTIDE WAS CO-CRYSTALLIZED WITH [E296Q]LTA4H BY LIQUID-LIQUID DIFFUSION IN MELTING-POINT CAPILLARIES. A TRIS-BUFFERED (10 mM, PH 7.5) SOLUTION OF PROTEIN AND TRIPEPTIDE, MOLAR RATIO 1:10 (~70 MICROM PROTEIN), WAS LAYERED ON THE PRECIPITATE SOLUTION CONTAINING 28% (WEIGHT/VOLUME) POLYETHYLENE GLYCOL (MW 8000), 50 mM NA ACETATE, 100 mM IMIDAZOLE, PH 6.8, AND 5 MM YBCL3. CRYSTALS WERE ADDITIONALLY SOAKED IN SOLUTIONS WITH INCREASED TRI-PEPTIDE CONCENTRATION PRIOR TO DATA COLLECTION., liquid-liquid diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 24, 2004
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.465→18.254 Å / Num. obs: 116485 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 7.8
Reflection shellResolution: 1.465→1.54 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.7 / Num. measured all: 58235 / Num. unique all: 15153 / Rsym value: 0.261 / % possible all: 88.4

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
SHELXrefinement
PDB_EXTRACT3data extraction
XFITdata reduction
SHELXL-97refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1H19

1h19


Resolution: 1.465→10 Å / Num. parameters: 49491 / Num. restraintsaints: 60634 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.023
RfactorNum. reflection% reflectionSelection details
Rfree0.169 3324 -RANDOM
Rwork0.128 ---
obs0.128 112248 100 %-
all-222475 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 17.362 Å2
Refinement stepCycle: LAST / Resolution: 1.465→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4906 0 12 605 5523
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.07
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.077
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.025
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.039
X-RAY DIFFRACTIONs_approx_iso_adps0.06
LS refinement shellResolution: 1.465→1.52 Å /
RfactorNum. reflection
Rwork0.189 -
obs-11226

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