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- PDB-7ev6: Crystal structure of the Lon-like protease MtaLonC with D581A mut... -

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Basic information

Entry
Database: PDB / ID: 7ev6
TitleCrystal structure of the Lon-like protease MtaLonC with D581A mutation in complex with F-b20-Q
Components
  • Endopeptidase La
  • F-b20-Q peptide {ortho-aminobenzoic acid (Abz)- QLRSLNGEWRFAWFPAPEAV[Tyr(3-NO2)]A}
KeywordsHYDROLASE / protease / TTC1975 peptidase / Lon-like protease
Function / homology
Function and homology information


endopeptidase La / ATP-dependent peptidase activity / protein catabolic process / serine-type endopeptidase activity / proteolysis / ATP binding
Similarity search - Function
Lon protease, AAA domain / LonB-like, AAA domain / LonB, AAA+ ATPase LID domain, archaeal-type / Archaeal LonB, AAA+ ATPase LID domain / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / endopeptidase La
Similarity search - Component
Biological speciesMeiothermus taiwanensis (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHsieh, K.Y. / Kuo, C.I. / Su, S.C. / Huang, K.F. / Chang, C.I.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)108-2320-B-001-011-MY3 Taiwan
Academia Sinica (Taiwan) Taiwan
CitationJournal: Sci Adv / Year: 2021
Title: Processive cleavage of substrate at individual proteolytic active sites of the Lon protease complex.
Authors: Shanshan Li / Kan-Yen Hsieh / Chiao-I Kuo / Shih-Chieh Su / Kai-Fa Huang / Kaiming Zhang / Chung-I Chang /
Abstract: The Lon protease is the prototype of a family of proteolytic machines with adenosine triphosphatase modules built into a substrate degradation chamber. Lon is known to degrade protein substrates in a ...The Lon protease is the prototype of a family of proteolytic machines with adenosine triphosphatase modules built into a substrate degradation chamber. Lon is known to degrade protein substrates in a processive fashion, cutting a protein chain processively into small peptides before commencing cleavages of another protein chain. Here, we present structural and biochemical evidence demonstrating that processive substrate degradation occurs at each of the six proteolytic active sites of Lon, which forms a deep groove that partially encloses the substrate polypeptide chain by accommodating only the unprimed residues and permits processive cleavage in the C-to-N direction. We identify a universally conserved acidic residue at the exit side of the binding groove indispensable for the proteolytic activity. This noncatalytic residue likely promotes processive proteolysis by carboxyl-carboxylate interactions with cleaved intermediates. Together, these results uncover a previously unrecognized mechanism for processive substrate degradation by the Lon protease.
History
DepositionMay 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Endopeptidase La
S: F-b20-Q peptide {ortho-aminobenzoic acid (Abz)- QLRSLNGEWRFAWFPAPEAV[Tyr(3-NO2)]A}
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2063
Polymers81,1112
Non-polymers951
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-11 kcal/mol
Surface area28040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.826, 115.826, 136.256
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-995-

HOH

21A-1008-

HOH

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Components

#1: Protein Endopeptidase La


Mass: 80514.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meiothermus taiwanensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: C9DRU9, endopeptidase La
#2: Protein/peptide F-b20-Q peptide {ortho-aminobenzoic acid (Abz)- QLRSLNGEWRFAWFPAPEAV[Tyr(3-NO2)]A}


Mass: 596.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 10% isopropanol, 100mM monosodium phosphate, 100mM sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Jun 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 57412 / % possible obs: 95.3 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 29.8
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 48926 / % possible all: 90.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FW9

4fw9


Resolution: 2.1→19.85 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.201 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.178 2600 5 %RANDOM
Rwork0.154 ---
obs0.156 48926 85.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.74 Å2 / Biso mean: 32.65 Å2 / Biso min: 8.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å20 Å2
2---1.05 Å20 Å2
3---2.1 Å2
Refinement stepCycle: final / Resolution: 2.1→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4602 0 5 427 5034
Biso mean--24.54 39.46 -
Num. residues----599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194703
X-RAY DIFFRACTIONr_bond_other_d0.0010.024563
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9876389
X-RAY DIFFRACTIONr_angle_other_deg0.7913.00110452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4865593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.322.905210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02815752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1641548
X-RAY DIFFRACTIONr_chiral_restr0.0730.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215347
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021067
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.16 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 108 -
Rwork0.227 1896 -
all-2004 -
obs--45.26 %

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