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Structure paper

TitleA 5+1 assemble-to-activate mechanism of the Lon proteolytic machine.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 7340, Year 2023
Publish dateNov 13, 2023
AuthorsShanshan Li / Kan-Yen Hsieh / Chiao-I Kuo / Tzu-Chi Lin / Szu-Hui Lee / Yi-Ru Chen / Chun-Hsiung Wang / Meng-Ru Ho / See-Yeun Ting / Kaiming Zhang / Chung-I Chang /
PubMed AbstractMany AAA+ (ATPases associated with diverse cellular activities) proteins function as protein or DNA remodelers by threading the substrate through the central pore of their hexameric assemblies. In ...Many AAA+ (ATPases associated with diverse cellular activities) proteins function as protein or DNA remodelers by threading the substrate through the central pore of their hexameric assemblies. In this ATP-dependent translocating state, the substrate is gripped by the pore loops of the ATPase domains arranged in a universal right-handed spiral staircase organization. However, the process by which a AAA+ protein is activated to adopt this substrate-pore-loop arrangement remains unknown. We show here, using cryo-electron microscopy (cryo-EM), that the activation process of the Lon AAA+ protease may involve a pentameric assembly and a substrate-dependent incorporation of the sixth protomer to form the substrate-pore-loop contacts seen in the translocating state. Based on the structural results, we design truncated monomeric mutants that inhibit Lon activity by binding to the native pentamer and demonstrated that expressing these monomeric mutants in Escherichia coli cells containing functional Lon elicits specific phenotypes associated with lon deficiency, including the inhibition of persister cell formation. These findings uncover a substrate-dependent assembly process for the activation of a AAA+ protein and demonstrate a targeted approach to selectively inhibit its function within cells.
External linksNat Commun / PubMed:37957149 / PubMed Central
MethodsEM (single particle)
Resolution3.4 - 5.8 Å
Structure data

EMDB-34000, PDB-7yph:
Open-spiral pentamer of the substrate-free Lon protease with a Y224S mutation
Method: EM (single particle) / Resolution: 3.68 Å

EMDB-34001, PDB-7ypi:
Spiral hexamer of the substrate-free Lon protease with a Y224S mutation
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-34002, PDB-7ypj:
Spiral pentamer of the substrate-free Lon protease with a S678A mutation
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-34003, PDB-7ypk:
Close-ring hexamer of the substrate-bound Lon protease with an S678A mutation
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-34004: Spiral hexamer of the substrate-free Lon protease with an S678A mutation
Method: EM (single particle) / Resolution: 4.7 Å

EMDB-34005: Open-spiral pentamer of the substrate-free Lon protease with Y397A and S678A mutations
Method: EM (single particle) / Resolution: 3.72 Å

EMDB-34006: Spiral hexamer of the substrate-free Lon protease with Y397A and S678A mutations
Method: EM (single particle) / Resolution: 4.08 Å

EMDB-34107, PDB-7yuh:
MtaLon-Apo for the spiral oligomers of trimer
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-34108, PDB-7yum:
MtaLon-Apo for the spiral oligomers of tetramer
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-34109, PDB-7yup:
MtaLon-Apo for the spiral oligomers of pentamer
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-34110, PDB-7yut:
MtaLon-Apo for the spiral oligomers of hexamer
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-34111, PDB-7yuu:
MtaLon-ADP for the spiral oligomers of trimer
Method: EM (single particle) / Resolution: 5.8 Å

EMDB-34112, PDB-7yuv:
MtaLon-ADP for the spiral oligomers of tetramer
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-34113, PDB-7yuw:
MtaLon-ADP for the spiral oligomers of pentamer
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-34114, PDB-7yux:
MtaLon-ADP for the spiral oligomers of hexamer
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-34116: Spiral pentamer of the substrate-free Lon protease with an M217A mutation
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-34117: Spiral hexamer of the substrate-free Lon protease with an M217A mutation
Method: EM (single particle) / Resolution: 5.3 Å

EMDB-36865: Spiral pentameric form of the substrate-free Lon protease with a Y224S mutation in the presence of the N-terminal-truncated monomeric mutant bearing an E613K mutation
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-36866: Spiral hexameric form of the substrate-free Lon protease with a Y224S mutation in the presence of the N-terminal-truncated monomeric mutant bearing an E613K mutation
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-36867, PDB-8k3y:
The "5+1" heteromeric structure of Lon protease consisting of a spiral pentamer with Y224S mutation and an N-terminal-truncated monomeric E613K mutant
Method: EM (single particle) / Resolution: 4.42 Å

Chemicals

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Source
  • meiothermus taiwanensis (bacteria)
  • bos taurus (cattle)
KeywordsHYDROLASE / Lon protease / hydrolysis / AAA proteins / AAA / protease / complex / proteolysis / Assembly / AAA+ protein / ATPase

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