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- PDB-1t7d: Crystal structure of Escherichia coli type I signal peptidase in ... -

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Basic information

Entry
Database: PDB / ID: 1t7d
TitleCrystal structure of Escherichia coli type I signal peptidase in complex with a lipopeptide inhibitor
Components
  • ARYLOMYCIN A2
  • SIGNAL PEPTIDASE I
KeywordsHYDROLASE/ANTIBIOTIC / SIGNAL PEPTIDASE / SER/LYS DYAD / HYDROLASE / LIPOPEPTIDE / ANTIBIOTIC / BIARYL BRIDGE / HYDROLASE-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


signal peptidase I / signal peptide processing / protein processing / peptidase activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / plasma membrane
Similarity search - Function
Signal Peptidase I; Chain: A, domain 2 / Signal Peptidase I; Chain: A, domain 2 - #10 / Signal peptidase I, all-beta subdomain / Peptidase S26A, signal peptidase I, lysine active site / Signal peptidases I lysine active site. / Peptidase S26A, signal peptidase I / Signal peptidase, peptidase S26 / Peptidase S26A, signal peptidase I, conserved site / Signal peptidases I signature 3. / Peptidase S26A, signal peptidase I, serine active site ...Signal Peptidase I; Chain: A, domain 2 / Signal Peptidase I; Chain: A, domain 2 - #10 / Signal peptidase I, all-beta subdomain / Peptidase S26A, signal peptidase I, lysine active site / Signal peptidases I lysine active site. / Peptidase S26A, signal peptidase I / Signal peptidase, peptidase S26 / Peptidase S26A, signal peptidase I, conserved site / Signal peptidases I signature 3. / Peptidase S26A, signal peptidase I, serine active site / Signal peptidases I serine active site. / Peptidase S26 / Umud Fragment, subunit A / Umud Fragment, subunit A / LexA/Signal peptidase-like superfamily / Beta Complex / Ribbon / Mainly Beta
Similarity search - Domain/homology
ARYLOMYCIN A2 / 10-METHYLUNDECANOIC ACID / : / Signal peptidase I
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
STREPTOMYCES TU (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsPaetzel, M. / Goodall, J.J. / Kania, M. / Dalbey, R.E. / Page, M.G.P.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Crystallographic and Biophysical Analysis of a Bacterial Signal Peptidase in Complex with a Lipopeptide Based Inhibitor.
Authors: Paetzel, M. / Goodall, J.J. / Kania, M. / Dalbey, R.E. / Page, M.G.P.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of a Bacterial Signal Peptidase Apoenzyme: Implications for Signal Peptide Binding and the Ser-Lys Dyad Mechanism
Authors: Paetzel, M. / Dalbey, R.E. / Strynadka, N.C.
#2: Journal: Nature / Year: 1998
Title: Crystal Structure of a Bacterial Signal Peptidase in Complex with a Beta-Lactam Inhibitor.
Authors: Paetzel, M. / Dalbey, R.E. / Strynadka, N.C.
History
DepositionMay 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 2.0Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIGNAL PEPTIDASE I
B: SIGNAL PEPTIDASE I
C: ARYLOMYCIN A2
D: ARYLOMYCIN A2
C: 10-METHYLUNDECANOIC ACID
D: 10-METHYLUNDECANOIC ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8506
Polymers57,4494
Non-polymers4012
Water4,774265
1
B: SIGNAL PEPTIDASE I
D: ARYLOMYCIN A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9253
Polymers28,7242
Non-polymers2001
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-4.5 kcal/mol
Surface area11140 Å2
MethodPISA
2
A: SIGNAL PEPTIDASE I
C: ARYLOMYCIN A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9253
Polymers28,7242
Non-polymers2001
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-4.6 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.609, 69.609, 258.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a monomer

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Components

#1: Protein SIGNAL PEPTIDASE I / SPASE I / LEADER PEPTIDASE I


Mass: 28079.814 Da / Num. of mol.: 2 / Fragment: RESIDUES 76-324
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Gene: LEPB / Plasmid: PET3D / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00803, signal peptidase I
#2: Protein/peptide ARYLOMYCIN A2


Type: Lipopeptide / Class: Antibiotic / Mass: 644.674 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ...Details: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ISO-C12 FATTY ACID IS LINKED TO RESIDUE 1.
Source: (natural) STREPTOMYCES TU (bacteria) / References: NOR: NOR01115, ARYLOMYCIN A2
#3: Chemical
ChemComp-M12 / 10-METHYLUNDECANOIC ACID


Type: Lipopeptide / Class: Antibiotic / Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
Details: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ...Details: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ISO-C12 FATTY ACID IS LINKED TO RESIDUE 1.
References: ARYLOMYCIN A2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Compound detailsARYLOMYCIN A2 IS A CYCLIC LIPOHEXAPEPTIDE, A MEMBER OF THE ARYLOMYCIN FAMILY. ALL MEMBERS HAVE A ...ARYLOMYCIN A2 IS A CYCLIC LIPOHEXAPEPTIDE, A MEMBER OF THE ARYLOMYCIN FAMILY. ALL MEMBERS HAVE A FATTY ACID AT THE N-TERM AND A CORE STRUCTURE OF TRIPEPTIDE MACROCYCLE FORMED BY A C-C BIARYL LINKAGE BETWEEN RESIDUES 4 AND 6. HERE, ARYLOMYCIN A2 IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND ONE LIGAND (HET) M12.
Sequence detailsTHE PROTEIN IS A SOLUBLE CATALYTICALLY ACTIVE FRAGMENT OF THE ESCHERICHIA COLI TYPE I SIGNAL ...THE PROTEIN IS A SOLUBLE CATALYTICALLY ACTIVE FRAGMENT OF THE ESCHERICHIA COLI TYPE I SIGNAL PEPTIDASE (DELTA 2-75). IT LACKS THE RESIDUES CORRESPONDING TO THE TWO TRANSMEMBRANE SEGMENTS (RESIDUES 4-28 AND 58-76) AND A SMALL CYTOPLASMIC REGION (RESIDUES 29-58).

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 6
Details: 0.5% TRITON X-100, 15% PEG 4000, 20% PROPANOL, 0.1 M SODIUM CITRATE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.47→40 Å / Num. obs: 21589 / % possible obs: 90.9 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 19.4
Reflection shellResolution: 2.47→2.56 Å / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 8 / % possible all: 86.4

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B12

1b12


Resolution: 2.47→29.54 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2098721.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2142 9.9 %RANDOM
Rwork0.23 ---
obs0.23 21584 90.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.11 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 49.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.48 Å20 Å20 Å2
2--6.48 Å20 Å2
3----12.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.47→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 6 265 3766
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.711.5
X-RAY DIFFRACTIONc_mcangle_it3.042
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 2.47→2.62 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 334 10.2 %
Rwork0.311 2952 -
obs--85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DRGCNS.PARDRGCNS.TOP

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