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- PDB-2fzs: Crystal structure of E. coli ClpP with a Peptide Chloromethyl Ket... -

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Basic information

Entry
Database: PDB / ID: 2fzs
TitleCrystal structure of E. coli ClpP with a Peptide Chloromethyl Ketone Covalently Bound at the Active Site
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / ATP-dependent ClpP protease / Z-Leu-Tyr Chloromethyl Ketone Inhibitor
Function / homology
Function and homology information


HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / ATP-dependent peptidase activity / proteasomal protein catabolic process / serine-type peptidase activity / response to radiation ...HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / ATP-dependent peptidase activity / proteasomal protein catabolic process / serine-type peptidase activity / response to radiation / ATPase binding / response to heat / serine-type endopeptidase activity / proteolysis / identical protein binding / membrane / cytosol
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-CMQ / TRIETHYLENE GLYCOL / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSzyk, A. / Maurizi, M.R.
CitationJournal: J.Struct.Biol. / Year: 2006
Title: Crystal structure at 1.9A of E. coli ClpP with a peptide covalently bound at the active site.
Authors: Szyk, A. / Maurizi, M.R.
History
DepositionFeb 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN THE BENZYLOXYCARBONYL-LEUCYLTYROSINE CHLOROMETHYL KETONE (Z-LEU-TYR-CMK) REACTS WITH CLPP ...HETEROGEN THE BENZYLOXYCARBONYL-LEUCYLTYROSINE CHLOROMETHYL KETONE (Z-LEU-TYR-CMK) REACTS WITH CLPP AND FORMS TWO COVALENT BONDS WITH SER97 AND HIS122 FROM ACTIVE SITE OF PROTEIN. THE HYDROXYL GROUP OF SER97 CREATE TETRAHEDRAL ADDUCT WITH THE KETONE CARBONYL CARBON OF THE INHIBITOR. THE NE2 IMIDAZOLE NITROGEN OF HIS122 IS COVALENTLY BOUND TO THE METHYLENE GROUP OF THE Z-LEU-TYR-CMK.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,48154
Polymers302,21614
Non-polymers9,26540
Water51,4332855
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area81680 Å2
ΔGint-180 kcal/mol
Surface area86480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.7, 101.0, 155.4
Angle α, β, γ (deg.)90.0, 99.0, 90.0
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetradecamer, present in the asymmetric unit

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Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp / Caseinolytic protease / Protease Ti / Heat shock protein F21.5


Mass: 21586.863 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12, MG1655 / Gene: clpP, lopP / Plasmid: pET3d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P0A6G7, endopeptidase Clp
#2: Chemical
ChemComp-CMQ / N~2~-[(BENZYLOXY)CARBONYL]-N-[(1S,2S)-2-HYDROXY-1-(4-HYDROXYBENZYL)PROPYL]-L-LEUCINAMIDE


Mass: 428.521 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C24H32N2O5
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2855 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M tri-sodium citrate, 0.15M ammonium acetate, 30% PEG 4000 , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.2547 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2004 / Details: mirrors
RadiationMonochromator: SI 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2547 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 215884 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2.8 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 1TYF

1tyf


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.889 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.233 10731 5 %RANDOM
Rwork0.173 ---
all0.176 203390 --
obs0.176 203390 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20.51 Å2
2--0.28 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20264 0 650 2855 23769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02221600
X-RAY DIFFRACTIONr_angle_refined_deg1.7872.00529004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08252564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96824.178955
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.177153954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.43415152
X-RAY DIFFRACTIONr_chiral_restr0.1260.23316
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215796
X-RAY DIFFRACTIONr_nbd_refined0.2230.212024
X-RAY DIFFRACTIONr_nbtor_refined0.3030.214948
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.22498
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.258
X-RAY DIFFRACTIONr_mcbond_it1.0461.513430
X-RAY DIFFRACTIONr_mcangle_it1.537220922
X-RAY DIFFRACTIONr_scbond_it2.76639146
X-RAY DIFFRACTIONr_scangle_it4.1764.58082
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 787 -
Rwork0.239 15261 -
obs--96.7 %
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)
11.2252-0.1201-0.11910.57510.15651.50290.0292-0.12170.1726-0.04280.0554-0.1046-0.13520.1269-0.0846-0.1682-0.0568-0.0108-0.2493-0.0611-0.078962.672681.647229.162
20.90860.0032-0.62730.6988-0.3971.2751-0.0357-0.30920.19160.03410.0676-0.0547-0.07330.3586-0.0319-0.196-0.0391-0.03420.0699-0.1637-0.112864.513876.591255.7796
30.74690.6651-0.03781.63840.17340.741-0.0607-0.14940.03460.14680.1052-0.13890.1590.3131-0.0444-0.16440.1016-0.06890.1977-0.0804-0.189965.530652.361168.2357
41.10630.00120.43290.57110.2411.327-0.1068-0.3223-0.01990.07650.0979-0.13330.28910.25490.00890.00370.2279-0.04140.0953-0.0081-0.183564.828927.353857.1525
51.1034-0.13630.01670.94530.2651.4491-0.1564-0.2434-0.03380.1690.2838-0.16170.22990.3204-0.1274-0.09140.129-0.0388-0.1176-0.0572-0.154862.916620.276530.9524
61.2998-0.6907-0.08911.867-0.11120.3665-0.07090.00330.008-0.03830.0969-0.17070.02080.0632-0.0261-0.1809-0.01350.0008-0.2745-0.0284-0.184361.350836.7379.2862
71.4318-0.0372-0.04361.24680.38770.7802-0.03430.02540.0622-0.0873-0.01-0.1305-0.04040.07220.0442-0.1548-0.03040.0015-0.2930.015-0.183661.320163.84598.5357
81.18140.0175-0.73920.5091-0.30811.8606-0.0397-0.1980.13960.0220.03690.0914-0.1683-0.23910.0028-0.16710.0648-0.0094-0.0249-0.1274-0.107619.900578.133656.0207
90.58140.1434-0.07761.42290.1220.7863-0.0868-0.153-0.02410.1551-0.05130.24170.1669-0.12430.1382-0.1375-0.00680.05860.0623-0.0634-0.145220.983955.465871.1408
101.17090.30230.36481.3230.67840.9694-0.0631-0.20340.01120.1578-0.01060.1810.2401-0.13680.07380.0025-0.02660.0988-0.05720.0505-0.169920.516829.552262.8231
111.2094-0.04950.0770.49050.27081.7428-0.0951-0.0884-0.1170.1390.02660.19120.2219-0.10190.0685-0.0487-0.0690.0687-0.21110.025-0.114518.732119.774537.5034
120.9798-0.34880.07551.1928-0.40261.1165-0.0343-0.0034-0.0323-0.0233-0.04030.18040.1378-0.16110.0746-0.2048-0.0432-0.0087-0.2263-0.0326-0.155616.99833.687214.1919
130.9498-0.3697-0.10951.63530.29310.6678-0.0941-0.00920.0702-0.0476-0.03170.1434-0.0209-0.20640.1258-0.19030.0098-0.0374-0.2178-0.0227-0.159516.640760.666210.3506
141.4904-0.3182-0.3550.83380.58061.5355-0.038-0.12490.136-0.0346-0.00660.0922-0.1601-0.23950.0447-0.16430.0647-0.0411-0.1705-0.0706-0.091618.036380.434829.0154
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA18 - 19218 - 192
2X-RAY DIFFRACTION1AO501
3X-RAY DIFFRACTION2BB18 - 19218 - 192
4X-RAY DIFFRACTION2BP502
5X-RAY DIFFRACTION3CC18 - 19218 - 192
6X-RAY DIFFRACTION3CQ503
7X-RAY DIFFRACTION4DD18 - 19218 - 192
8X-RAY DIFFRACTION4DR504
9X-RAY DIFFRACTION5EE18 - 19218 - 192
10X-RAY DIFFRACTION5ES505
11X-RAY DIFFRACTION6FF18 - 19218 - 192
12X-RAY DIFFRACTION6FT506
13X-RAY DIFFRACTION7GG18 - 19218 - 192
14X-RAY DIFFRACTION7GU507
15X-RAY DIFFRACTION8HH18 - 19218 - 192
16X-RAY DIFFRACTION8HV508
17X-RAY DIFFRACTION9II18 - 19218 - 192
18X-RAY DIFFRACTION9IW509
19X-RAY DIFFRACTION10JJ18 - 19218 - 192
20X-RAY DIFFRACTION10JX510
21X-RAY DIFFRACTION11KK18 - 19218 - 192
22X-RAY DIFFRACTION11KY511
23X-RAY DIFFRACTION12LL18 - 19218 - 192
24X-RAY DIFFRACTION12LZ512
25X-RAY DIFFRACTION13MM18 - 19218 - 192
26X-RAY DIFFRACTION13MAA513
27X-RAY DIFFRACTION14NN18 - 19218 - 192
28X-RAY DIFFRACTION14NBA514

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