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Basic information

Entry
Database: PDB / ID: 7fid
TitleProcessive cleavage of substrate at individual proteolytic active sites of the Lon proteasecomplex (conformation 1)
Components
  • Lon protease
  • unknown endogenous substrate
KeywordsHYDROLASE / AAA / protease / complex / proteolysis
Function / homology
Function and homology information


endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / cellular response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5270 / LON domain-like / Lon protease, bacterial / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / : / Lon protease, bacterial/eukaryotic-type / Lon protease AAA+ ATPase lid domain / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5270 / LON domain-like / Lon protease, bacterial / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / : / Lon protease, bacterial/eukaryotic-type / Lon protease AAA+ ATPase lid domain / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / Helicase, Ruva Protein; domain 3 - #60 / Ribosomal Protein S5; domain 2 - #10 / PUA-like superfamily / Ribosomal Protein S5; domain 2 / Helicase, Ruva Protein; domain 3 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ribosomal protein S5 domain 2-type fold, subgroup / Roll / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Lon protease
Similarity search - Component
Biological speciesMeiothermus taiwanensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.44 Å
AuthorsLi, S. / Hsieh, K. / Kuo, C. / Su, S. / Huang, K. / Zhang, K. / Chang, C.I.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)108-2320-B-001-011-MY3 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
DepositionJul 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.0Nov 24, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 24, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 24, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 24, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 24, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
B: Lon protease
C: Lon protease
D: Lon protease
E: Lon protease
F: Lon protease
A: Lon protease
S: unknown endogenous substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)545,23013
Polymers542,3787
Non-polymers2,8516
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area45480 Å2
ΔGint-129 kcal/mol
Surface area219990 Å2

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Components

#1: Protein
Lon protease / ATP-dependent protease La


Mass: 90081.336 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meiothermus taiwanensis (bacteria) / Gene: lonA1, lon / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059VAZ3, endopeptidase La
#2: Protein/peptide unknown endogenous substrate


Mass: 1890.321 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)
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Lon bound to endogenous substrate / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.6 MDa / Experimental value: YES
Source (natural)Organism: Meiothermus taiwanensis WR-220 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 48 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
8PHENIXmodel refinement
12cryoSPARCclassification
13cryoSPARC33D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 324693 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00937676
ELECTRON MICROSCOPYf_angle_d1.07251120
ELECTRON MICROSCOPYf_dihedral_angle_d5.57723238
ELECTRON MICROSCOPYf_chiral_restr0.0635830
ELECTRON MICROSCOPYf_plane_restr0.0096634

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