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- PDB-5e7s: Hexameric structure of a LonA protease domain in active state -

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Basic information

Entry
Database: PDB / ID: 5e7s
TitleHexameric structure of a LonA protease domain in active state
ComponentsLon protease
KeywordsHYDROLASE / AAA+ domain / Lon protease / protease domain
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
Lon protease, bacterial / : / 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 protease, bacterial / : / 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 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMeiothermus taiwanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsLin, C.-C. / Su, S.-C. / Chang, C.-I.
CitationJournal: Structure / Year: 2016
Title: Structural Basis for the Magnesium-Dependent Activation and Hexamerization of the Lon AAA+ Protease.
Authors: Shih-Chieh Su / Chien-Chu Lin / Hui-Chung Tai / Mu-Yueh Chang / Meng-Ru Ho / C Satheesan Babu / Jiahn-Haur Liao / Shih-Hsiung Wu / Yuan-Chih Chang / Carmay Lim / Chung-I Chang /
Abstract: The Lon AAA+ protease (LonA) plays important roles in protein homeostasis and regulation of diverse biological processes. LonA behaves as a homomeric hexamer in the presence of magnesium (Mg(2+)) and ...The Lon AAA+ protease (LonA) plays important roles in protein homeostasis and regulation of diverse biological processes. LonA behaves as a homomeric hexamer in the presence of magnesium (Mg(2+)) and performs ATP-dependent proteolysis. However, it is also found that LonA can carry out Mg(2+)-dependent degradation of unfolded protein substrate in an ATP-independent manner. Here we show that in the presence of Mg(2+) LonA forms a non-secluded hexameric barrel with prominent openings, which explains why Mg(2+)-activated LonA can operate as a diffusion-based chambered protease to degrade unstructured protein and peptide substrates efficiently in the absence of ATP. A 1.85 Å crystal structure of Mg(2+)-activated protease domain reveals Mg(2+)-dependent remodeling of a substrate-binding loop and a potential metal-binding site near the Ser-Lys catalytic dyad, supported by biophysical binding assays and molecular dynamics simulations. Together, these findings reveal the specific roles of Mg(2+) in the molecular assembly and activation of LonA.
History
DepositionOct 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references / Experimental preparation
Revision 1.3Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lon protease
B: Lon protease
C: Lon protease
D: Lon protease
E: Lon protease
F: Lon protease
G: Lon protease
H: Lon protease
I: Lon protease
J: Lon protease
K: Lon protease
L: Lon protease


Theoretical massNumber of molelcules
Total (without water)391,25212
Polymers391,25212
Non-polymers00
Water00
1
A: Lon protease
B: Lon protease
C: Lon protease
D: Lon protease
E: Lon protease
F: Lon protease

A: Lon protease
B: Lon protease
C: Lon protease
D: Lon protease
E: Lon protease
F: Lon protease


Theoretical massNumber of molelcules
Total (without water)391,25212
Polymers391,25212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area27240 Å2
ΔGint-92 kcal/mol
Surface area143710 Å2
MethodPISA
2
G: Lon protease
H: Lon protease
I: Lon protease
J: Lon protease
K: Lon protease
L: Lon protease

G: Lon protease
H: Lon protease
I: Lon protease
J: Lon protease
K: Lon protease
L: Lon protease


Theoretical massNumber of molelcules
Total (without water)391,25212
Polymers391,25212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_856-x+3,y,-z+11
Buried area26300 Å2
ΔGint-97 kcal/mol
Surface area145610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.309, 212.787, 178.921
Angle α, β, γ (deg.)90.00, 100.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 32604.346 Da / Num. of mol.: 12 / Fragment: UNP residues 491-781
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

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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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 6.5 / Details: 0.2M sodium citrate pH6.5, 12% PEG 3350

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.8 Å
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: Jun 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 3.03→175.8 Å / Num. obs: 74605 / % possible obs: 90.92 % / Redundancy: 4.7 % / Net I/σ(I): 16.7
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.33 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YPM

4ypm


Resolution: 3.03→20 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.871 / SU B: 23.78 / SU ML: 0.415 / Cross valid method: THROUGHOUT / ESU R Free: 0.542 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 3798 5.1 %RANDOM
Rwork0.227 ---
obs0.23 70806 90.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.63 Å2
2---0.65 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 3.03→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26292 0 0 0 26292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01926800
X-RAY DIFFRACTIONr_bond_other_d0.0010.0226451
X-RAY DIFFRACTIONr_angle_refined_deg0.9471.99436356
X-RAY DIFFRACTIONr_angle_other_deg0.722361110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.24753431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56424.1641064
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.523154712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.64215191
X-RAY DIFFRACTIONr_chiral_restr0.0510.24130
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02129903
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025352
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_mcbond_it0.8447.213760
X-RAY DIFFRACTIONr_mcbond_other0.8447.19913759
X-RAY DIFFRACTIONr_mcangle_it1.59310.79417176
X-RAY DIFFRACTIONr_mcangle_other1.59310.79417177
X-RAY DIFFRACTIONr_scbond_it0.4217.38913039
X-RAY DIFFRACTIONr_scbond_other0.4217.38913040
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.91611.04519180
X-RAY DIFFRACTIONr_long_range_B_refined2.77456.58928468
X-RAY DIFFRACTIONr_long_range_B_other2.77456.59228469
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.03→3.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 174 -
Rwork0.319 3226 -
obs--57.57 %

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