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- PDB-6lt4: AAA+ ATPase, ClpL from Streptococcus pneumoniae: ATPrS-bound -

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Basic information

Entry
Database: PDB / ID: 6lt4
TitleAAA+ ATPase, ClpL from Streptococcus pneumoniae: ATPrS-bound
ComponentsATP-dependent Clp protease, ATP-binding subunit
KeywordsCHAPERONE / AAA+ ATPase / ClpL / Streptococcus pneumoniae
Function / homology
Function and homology information


peptidase activity / cellular response to heat / ATP hydrolysis activity / proteolysis / ATP binding / cytoplasm
Similarity search - Function
UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/ClpB, AAA lid domain / AAA lid domain / : / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) ...UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/ClpB, AAA lid domain / AAA lid domain / : / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-dependent Clp protease, ATP-binding subunit
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsKim, G. / Lee, S.G. / Han, S. / Jung, J. / Jeong, H.S. / Hyun, J.K. / Rhee, D.K. / Kim, H.M. / Lee, S.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1A2B6004367 Korea, Republic Of
National Research Foundation (NRF, Korea)2017R1A5A1014560 Korea, Republic Of
Rural Development AdministrationPJ01367602 Korea, Republic Of
CitationJournal: FASEB J / Year: 2020
Title: ClpL is a functionally active tetradecameric AAA+ chaperone, distinct from hexameric/dodecameric ones.
Authors: Gyuhee Kim / Seong-Gyu Lee / Seungsu Han / Jaeeun Jung / Hyeong Seop Jeong / Jae-Kyung Hyun / Dong-Kwon Rhee / Ho Min Kim / Sangho Lee /
Abstract: AAA+ (ATPases associated with diverse cellular activities) chaperones are involved in a plethora of cellular activities to ensure protein homeostasis. The function of AAA+ chaperones is mostly ...AAA+ (ATPases associated with diverse cellular activities) chaperones are involved in a plethora of cellular activities to ensure protein homeostasis. The function of AAA+ chaperones is mostly modulated by their hexameric/dodecameric quaternary structures. Here we report the structural and biochemical characterizations of a tetradecameric AAA+ chaperone, ClpL from Streptococcus pneumoniae. ClpL exists as a tetradecamer in solution in the presence of ATP. The cryo-EM structure of ClpL at 4.5 Å resolution reveals a striking tetradecameric arrangement. Solution structures of ClpL derived from small-angle X-ray scattering data suggest that the tetradecameric ClpL could assume a spiral conformation found in active hexameric/dodecameric AAA+ chaperone structures. Vertical positioning of the middle domain accounts for the head-to-head arrangement of two heptameric rings. Biochemical activity assays with site-directed mutagenesis confirmed the critical roles of residues both in the integrity of the tetradecameric arrangement and activities of ClpL. Non-conserved Q321 and R670 are crucial in the heptameric ring assembly of ClpL. These results establish that ClpL is a functionally active tetradecamer, clearly distinct from hexameric/dodecameric AAA+ chaperones.
History
DepositionJan 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)1,101,71970
Polymers1,086,38714
Non-polymers15,33156
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
ATP-dependent Clp protease, ATP-binding subunit


Mass: 77599.094 Da / Num. of mol.: 14 / Mutation: E193A/E526A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria)
Gene: clpL, SPD_0308 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2ZMB9
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#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.: 28 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
Has ligand of interestY

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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: AAA+ ATPase, chaperone / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 1.1 MDa / Experimental value: YES
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: DARK FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: phenix.real_space_refine / Version: 1.18.2_3874 / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49797 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 118.27 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005569300
ELECTRON MICROSCOPYf_angle_d0.831493926
ELECTRON MICROSCOPYf_chiral_restr0.047610962
ELECTRON MICROSCOPYf_plane_restr0.003912320
ELECTRON MICROSCOPYf_dihedral_angle_d11.50019660

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