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- PDB-3cs0: Crystal structure of DegP24 -

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Basic information

Entry
Database: PDB / ID: 3cs0
TitleCrystal structure of DegP24
Components
  • Periplasmic serine endoprotease DegP
  • pentapeptide
KeywordsHYDROLASE / DegP / HtrA / protease / chaperone / PDZ / outer membrane protein / OMP / periplasm
Function / homology
Function and homology information


peptidase Do / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / serine-type peptidase activity / protein folding / outer membrane-bounded periplasmic space / peptidase activity / response to heat / response to oxidative stress ...peptidase Do / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / serine-type peptidase activity / protein folding / outer membrane-bounded periplasmic space / peptidase activity / response to heat / response to oxidative stress / periplasmic space / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Peptidase S1C, Do / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily ...Peptidase S1C, Do / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Periplasmic serine endoprotease DegP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 3 Å
AuthorsKrojer, T. / Sawa, J. / Schaefer, E. / Saibil, H.R. / Ehrmann, M. / Clausen, T.
CitationJournal: Nature / Year: 2008
Title: Structural basis for the regulated protease and chaperone function of DegP.
Authors: Tobias Krojer / Justyna Sawa / Eva Schäfer / Helen R Saibil / Michael Ehrmann / Tim Clausen /
Abstract: All organisms have to monitor the folding state of cellular proteins precisely. The heat-shock protein DegP is a protein quality control factor in the bacterial envelope that is involved in ...All organisms have to monitor the folding state of cellular proteins precisely. The heat-shock protein DegP is a protein quality control factor in the bacterial envelope that is involved in eliminating misfolded proteins and in the biogenesis of outer-membrane proteins. Here we describe the molecular mechanisms underlying the regulated protease and chaperone function of DegP from Escherichia coli. We show that binding of misfolded proteins transforms hexameric DegP into large, catalytically active 12-meric and 24-meric multimers. A structural analysis of these particles revealed that DegP represents a protein packaging device whose central compartment is adaptable to the size and concentration of substrate. Moreover, the inner cavity serves antagonistic functions. Whereas the encapsulation of folded protomers of outer-membrane proteins is protective and might allow safe transit through the periplasm, misfolded proteins are eliminated in the molecular reaction chamber. Oligomer reassembly and concomitant activation on substrate binding may also be critical in regulating other HtrA proteases implicated in protein-folding diseases.
History
DepositionApr 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 13, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref / struct_ref_seq_dif
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_mutation / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_mod_residue.details / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.pdbx_align_begin

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic serine endoprotease DegP
B: pentapeptide


Theoretical massNumber of molelcules
Total (without water)47,9532
Polymers47,9532
Non-polymers00
Water0
1
A: Periplasmic serine endoprotease DegP
B: pentapeptide
x 24


Theoretical massNumber of molelcules
Total (without water)1,150,87248
Polymers1,150,87248
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation24_555-z,-y,-x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation21_555z,y,-x1
Buried area88590 Å2
ΔGint-546 kcal/mol
Surface area374200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)253.929, 253.929, 253.929
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432

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Components

#1: Protein Periplasmic serine endoprotease DegP / E.C.3.4.21.- / Heat shock protein DegP / Protease Do


Mass: 47509.449 Da / Num. of mol.: 1 / Mutation: S210A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: degP, htrA, ptd, b0161, JW0157 / Production host: Escherichia coli (strain K12) (bacteria) / Strain (production host): K12 / References: UniProt: P0C0V0, peptidase Do
#2: Protein/peptide pentapeptide


Mass: 443.539 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (strain K12) (bacteria)

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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: 3.56 Å3/Da / Density % sol: 65.41 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8.5
Details: PEG 550 MME, NaCl, pH 8.5, vapor diffusion, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2006
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 12.96 / Number: 134848 / Rmerge(I) obs: 0.093 / D res high: 3 Å / Num. obs: 26475 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
8.6830108797.110.034
6.278.68181699.710.047
5.166.27230810010.056
4.485.16275310010.056
4.024.48304499.810.072
3.684.02334199.910.114
3.413.68369399.810.174
3.193.41395799.710.319
33.19447699.910.579
ReflectionResolution: 3→30 Å / Num. obs: 26475 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 60.25 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.96
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3-3.190.579322964447699.9
3.19-3.410.3195.220342395799.7
3.41-3.680.1748.418976369399.8
3.68-4.020.11412.717153334199.9
4.02-4.480.07217.815524304499.8
4.48-5.160.05620.9139942753100
5.16-6.270.05621115812308100
6.27-8.680.04724.59003181699.7
8.68-300.03428.65311108797.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameClassification
DNAdata collection
SHARPphasing
CNSrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 727 5 %RANDOM
Rwork0.212 ---
all-14441 --
obs-14441 99.9 %-
Solvent computationBsol: 28.863 Å2
Displacement parametersBiso mean: 68.999 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 0 0 2893
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.531
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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