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- PDB-1uoq: PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, S554A MUTANT WITH BOUND... -

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Basic information

Entry
Database: PDB / ID: 1uoq
TitlePROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, S554A MUTANT WITH BOUND PEPTIDE LIGAND GLU-PHE-SER-PRO
Components
  • PEPTIDE LIGAND GLU-PHE-SER-PRO
  • PROLYL ENDOPEPTIDASE
KeywordsHYDROLASE / PROLYL OLIGOPEPTIDASE / AMNESIA / ALPHA/ BETA-HYDROLASE / BETA-PROPELLER / SERINE PROTEASE
Function / homology
Function and homology information


prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytosol / cytoplasm
Similarity search - Function
Prolyl oligopeptidase, N-terminal domain / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H ...Prolyl oligopeptidase, N-terminal domain / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Prolyl endopeptidase
Similarity search - Component
Biological speciesSUS SCROFA (pig)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRea, D. / Fulop, V.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Electrostatic Environment at the Active Site of Prolyl Oligopeptidase is Highly Influential During Substrate Binding
Authors: Szeltner, Z. / Rea, D. / Renner, V. / Juliano, L. / Fulop, V. / Polgar, L.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Electrostatic Effects and Binding Determinants in the Catalysis of Prolyl Oligopeptidase: Site Specific Mutagenesis at the Oxyanion Binding Site
Authors: Szeltner, Z. / Rea, D. / Renner, V. / Fulop, V. / Polgar, L.
#2: Journal: J.Biol.Chem. / Year: 2002
Title: Substrate-Dependent Competency of the Catalytic Triad of Prolyl Oligopeptidase
Authors: Szeltner, Z. / Rea, D. / Juhasz, T. / Renner, V. / Mucsi, Z. / Orosz, G. / Fulop, V. / Polgar, L.
#3: Journal: J.Biol.Chem. / Year: 2001
Title: Structures of Prolyl Oligopeptidase Substrate/ Inhibitor Complexes. Use of Inhibitor Binding for Titration of the Catalytic Histidine Residue
Authors: Fulop, V. / Szeltner, Z. / Renner, V. / Polgar, L.
#4: Journal: Embo Rep. / Year: 2000
Title: Catalysis of Serine Oligopeptidases is Controlled by a Gating Filter Mechanism
Authors: Fulop, V. / Szeltner, Z. / Polgar, L.
#5: Journal: Cell(Cambridge,Mass.) / Year: 1998
Title: Prolyl Oligopeptidase: An Unusual Beta-Propeller Domain Regulates Proteolysis
Authors: Fulop, V. / Bocskei, Z.
History
DepositionSep 22, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2003Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROLYL ENDOPEPTIDASE
B: PEPTIDE LIGAND GLU-PHE-SER-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5114
Polymers81,3272
Non-polymers1842
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.300, 99.100, 109.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE DIMERIC ASSEMBLY DESCRIBED HERE IS DUE TO A COMPLEXOF THE PROTEIN CHAIN A WITH A PEPTIDE (CHAIN B). CHAIN AIS ESSENTIALLY A MONOMER IN THE PHYSIOLOGICAL STATE.

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Components

#1: Protein PROLYL ENDOPEPTIDASE / POST-PROLINE CLEAVING ENZYME / PE / PREP


Mass: 80848.344 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ENGINEERED MUTATION SER 554 ALA / Source: (gene. exp.) SUS SCROFA (pig) / Tissue: BRAIN / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P23687, prolyl oligopeptidase
#2: Protein/peptide PEPTIDE LIGAND GLU-PHE-SER-PRO


Mass: 478.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#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.: 532 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN A, SER 554 ALA THE MUTATED REGION CORREPONDS TO THE ACT_SITE CHARGE ...ENGINEERED MUTATION IN CHAIN A, SER 554 ALA THE MUTATED REGION CORREPONDS TO THE ACT_SITE CHARGE RELAY OF THE SEQUENCE CLEAVES PEPTIDE BONDS ON THE C-TERMINAL SIDE OF PROLYL RESIDUES WITHIN PEPTIDES OF UP TO APPROXIMATELY 30 AMINO ACIDS IN LENGTH. BELONGS TO PEPTIDASE FAMILY S9A. CATALYTIC ACTIVITY: HYDROLYSIS OF PRO-|-XAA >> ALA-|-XAA IN OLIGOPEPTIDES.

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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: 2.5 Å3/Da / Density % sol: 44 %
Crystal growpH: 8.5 / Details: SEE REFERENCE 5, pH 8.50
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Fulop, V., (1998) Cell(Cambridge,Mass.), 94, 161.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 %(w/v)mPEG50001reservoir
215 %(v/v)glycerol1reservoir
31 %(v/v)monothioglycerol1reservoir
420 mM1reservoirCa(Ac)2
5100 mMTris1reservoir
610 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: May 9, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.1→36 Å / Num. obs: 43221 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 3.7 / % possible all: 76.8
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 36 Å / Num. measured all: 153386 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
Lowest resolution: 2.15 Å / % possible obs: 76.8 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H2Z

1h2z


Resolution: 2.1→36 Å / SU B: 3.663 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.173
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1827 4 %RANDOM
Rwork0.147 ---
obs0.149 41394 95.1 %-
Displacement parametersBiso mean: 26.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2---1.67 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5734 0 12 532 6278
Refinement
*PLUS
% reflection Rfree: 4 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.026
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.9
LS refinement shell
*PLUS
Rfactor Rfree: 0.234 / Num. reflection Rfree: 101 / Rfactor Rwork: 0.145 / Num. reflection obs: 2376

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