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- PDB-2bkl: Structural and Mechanistic Analysis of Two Prolyl Endopeptidases:... -

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Basic information

Entry
Database: PDB / ID: 2bkl
TitleStructural and Mechanistic Analysis of Two Prolyl Endopeptidases: Role of Inter-Domain Dynamics in Catalysis and Specificity
ComponentsPROLYL ENDOPEPTIDASE
KeywordsHYDROLASE / PROLYL ENDOPEPTIDASE / MECHANISTIC STUDY / CELIAC SPRUE / PROTEASE
Function / homology
Function and homology information


prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytosol
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 ...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
N-[(BENZYLOXY)CARBONYL]-L-ALANYL-L-PROLINE / prolyl oligopeptidase
Similarity search - Component
Biological speciesMYXOCOCCUS XANTHUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKhosla, C. / Shan, L. / Mathews, I.I.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structural and Mechanistic Analysis of Two Prolyl Endopeptidases: Role of Interdomain Dynamics in Catalysis and Specificity
Authors: Shan, L. / Mathews, I.I. / Khosla, C.
#1: Journal: Biochem.J. / Year: 2004
Title: Comparative Biochemical Analysis of Three Bacterial Prolyl Endopeptidases: Implications for Celiac Sprue
Authors: Shan, L. / Marti, T. / Sollid, L.M. / Gray, G.M. / Khosla, C.
#2: Journal: Science / Year: 2002
Title: Structural Basis for Gluten Intolerance in Celiac Sprue
Authors: Shan, L. / Molberg, O. / Parrot, I. / Hausch, F. / Filiz, F. / Gray, G.M. / Sollid, L.M. / Khosla, C.
#3: Journal: Cell.Mol.Life.Sci. / Year: 2002
Title: The Prolyl Oligopeptidase Family
Authors: Polgar, L.
History
DepositionFeb 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms ...pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
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

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Assembly

Deposited unit
A: PROLYL ENDOPEPTIDASE
B: PROLYL ENDOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,1989
Polymers155,5552
Non-polymers1,6437
Water24,6991371
1
A: PROLYL ENDOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5845
Polymers77,7771
Non-polymers8074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROLYL ENDOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6134
Polymers77,7771
Non-polymers8363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.692, 114.718, 99.279
Angle α, β, γ (deg.)90.00, 103.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROLYL ENDOPEPTIDASE


Mass: 77777.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Z-ALA PROLINAL / Source: (gene. exp.) MYXOCOCCUS XANTHUS (bacteria) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9X5N2, prolyl oligopeptidase
#2: Chemical ChemComp-ZAH / N-[(BENZYLOXY)CARBONYL]-L-ALANYL-L-PROLINE / Z-ALA PROLINAL


Mass: 320.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H20N2O5
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1371 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 45 %
Crystal growpH: 6 / Details: 26% METHOXY PEG 5K AND 0.1MES (PH 6.01).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 19, 2003
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 225366 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.8 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QFS

1qfs


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.062 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME OF THE RESIDUES ARE MODELED WITH ALTERNATE CONFORMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.182 11252 5 %RANDOM
Rwork0.16 ---
obs0.161 214057 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å2-0.01 Å2
2--0.47 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10717 0 108 1371 12196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02111137
X-RAY DIFFRACTIONr_bond_other_d0.0020.029844
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.95115138
X-RAY DIFFRACTIONr_angle_other_deg1.235322909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1651351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.21593
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212455
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022368
X-RAY DIFFRACTIONr_nbd_refined0.2090.21825
X-RAY DIFFRACTIONr_nbd_other0.2570.211376
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.26418
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2925
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0770.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4322.56733
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.385410824
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.34254404
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.11434312
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.256 812
Rwork0.224 15555
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.29380.0352-0.02490.2731-0.01550.17520.01110.00110.0002-0.0126-0.00820.0128-0.01870.0484-0.0030.0298-0.0005-0.00190.04730.01020.0215-37.74487.47940.8975
20.38680.0469-0.15210.1420.010.25060.0144-0.0626-0.04670.0034-0.01960.0232-0.00520.01840.00520.0271-0.00850.00090.02390.01980.032-55.2967-7.198521.2116
30.2407-0.01690.00030.210.06440.3014-0.0096-0.0029-0.01030.0118-0.0258-0.0049-0.0198-0.04950.03540.0354-0.0014-0.00080.0345-0.00720.0264-32.5773.02565.1799
40.1885-0.0217-0.04440.25050.11940.4039-0.01170.0405-0.02430.0334-0.0012-0.00860.06330.01350.01290.0380.00480.00480.0058-0.01310.0393-16.7938-19.430151.6331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 68
2X-RAY DIFFRACTION1A409 - 677
3X-RAY DIFFRACTION2A69 - 408
4X-RAY DIFFRACTION3B2 - 68
5X-RAY DIFFRACTION3B409 - 678
6X-RAY DIFFRACTION4B69 - 408

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