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- PDB-2r3y: Crystal structure of the DegS protease in complex with the YWF ac... -

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Basic information

Entry
Database: PDB / ID: 2r3y
TitleCrystal structure of the DegS protease in complex with the YWF activating peptide
Components
  • Protease degS
  • Synthetic peptide YWF
Keywordshydrolase/hydrolase activator / reversible activation of a protease / catalytic triad / Hydrolase / Periplasm / Serine protease / hydrolase-hydrolase activator COMPLEX
Function / homology
Function and homology information


peptidase Do / cellular response to misfolded protein / serine-type peptidase activity / peptidase activity / outer membrane-bounded periplasmic space / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Peptidase S1C, DegS / PDZ domain / 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 ...Peptidase S1C, DegS / PDZ domain / 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 / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine endoprotease DegS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsClausen, T. / Hasselblatt, H.
CitationJournal: Genes Dev. / Year: 2007
Title: Regulation of the sigmaE stress response by DegS: how the PDZ domain keeps the protease inactive in the resting state and allows integration of different OMP-derived stress signals upon folding stress.
Authors: Hasselblatt, H. / Kurzbauer, R. / Wilken, C. / Krojer, T. / Sawa, J. / Kurt, J. / Kirk, R. / Hasenbein, S. / Ehrmann, M. / Clausen, T.
History
DepositionAug 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease degS
B: Protease degS
C: Protease degS
D: Synthetic peptide YWF
E: Synthetic peptide YWF
F: Synthetic peptide YWF


Theoretical massNumber of molelcules
Total (without water)103,5816
Polymers103,5816
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.800, 142.700, 41.100
Angle α, β, γ (deg.)90.00, 90.68, 90.00
Int Tables number5
Space group name H-MC121
DetailsOne homotrimer of DegS was observed in the asymmetric unit and should represent its physiological state.

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Components

#1: Protein Protease degS


Mass: 33243.664 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: degS, hhoB, htrH / Plasmid: pET15-b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0AEE3, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide Synthetic peptide YWF


Mass: 1283.455 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: The YWF peptide mimics the C-terminus of Outer Membrane Proteins.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The YWF (100 microM) was added to DegS and incubated 30 minutes before setting up the co-crystallization trials. Crystals of the complex were grown in sitting drops at 19 C by mixing 4 ...Details: The YWF (100 microM) was added to DegS and incubated 30 minutes before setting up the co-crystallization trials. Crystals of the complex were grown in sitting drops at 19 C by mixing 4 microL of DegS/YWF with 2 microL of a crystallization solution containing 0.1 M HEPES (pH 7.5), 6% PEG 6000, 9% MPD and 10 mM MgCl2. Crystal trials were set up in cryschem plates with a reservoir volume of 400 microL. , VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 30, 2006 / Details: mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 39228 / Num. obs: 39228 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 60 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.047 / Net I/σ(I): 13.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / Num. unique all: 3644 / Rsym value: 0.33 / % possible all: 88.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1soz

1soz


Resolution: 2.5→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1923 -random
Rwork0.204 ---
all0.208 38774 --
obs0.208 38774 95 %-
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6292 0 0 157 6449
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.45

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