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- PDB-8osg: AAA+ motor subunit ChlI of magnesium chelatase, hexamer conformation B -

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Basic information

Entry
Database: PDB / ID: 8osg
TitleAAA+ motor subunit ChlI of magnesium chelatase, hexamer conformation B
ComponentsMagnesium-chelatase subunit ChlI
KeywordsPHOTOSYNTHESIS / AAA+ / Magnesium Chelatase / Cyanobacteria
Function / homology
Function and homology information


magnesium chelatase / magnesium chelatase activity / chlorophyll biosynthetic process / photosynthesis / ATP hydrolysis activity / ATP binding
Similarity search - Function
Magnesium-chelatase subunit ChlI-like / Magnesium chelatase, ATPase subunit I / ChlI/MoxR, AAA lid domain / AAA lid domain / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Magnesium-chelatase subunit ChlI
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsShvarev, D. / Moeller, A.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC 944 Germany
German Research Foundation (DFG)CRC1557 Germany
German Research Foundation (DFG)INST 190/196-1 FUGG Germany
German Federal Ministry for Education and ResearchJPND-DLR 01ED2010 Germany
CitationJournal: mBio / Year: 2023
Title: Conformational variability of cyanobacterial ChlI, the AAA+ motor of magnesium chelatase involved in chlorophyll biosynthesis.
Authors: Dmitry Shvarev / Alischa Ira Scholz / Arne Moeller /
Abstract: Photosynthesis is an essential life process that relies on chlorophyll. In photosynthetic organisms, chlorophyll synthesis involves multiple steps and depends on magnesium chelatase. This enzyme ...Photosynthesis is an essential life process that relies on chlorophyll. In photosynthetic organisms, chlorophyll synthesis involves multiple steps and depends on magnesium chelatase. This enzyme complex is responsible for inserting magnesium into the chlorophyll precursor, but the molecular mechanism of this process is not fully understood. By using cryogenic electron microscopy and conducting functional analyses, we have discovered that the motor subunit ChlI of magnesium chelatase undergoes conformational changes in the presence of ATP. Our findings offer new insights into how energy is transferred from ChlI to the other components of magnesium chelatase. This information significantly contributes to our understanding of the initial step in chlorophyll biosynthesis and lays the foundation for future studies on the entire process of chlorophyll production.
History
DepositionApr 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Magnesium-chelatase subunit ChlI
B: Magnesium-chelatase subunit ChlI
C: Magnesium-chelatase subunit ChlI
D: Magnesium-chelatase subunit ChlI
E: Magnesium-chelatase subunit ChlI
F: Magnesium-chelatase subunit ChlI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,73616
Polymers252,7566
Non-polymers2,98010
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Magnesium-chelatase subunit ChlI / Mg-protoporphyrin IX chelatase


Mass: 42125.930 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Gene: chlI, all0152 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P58571, magnesium chelatase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*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: ChlI in the presence of ATP / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
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

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20_4459: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80344 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00214756
ELECTRON MICROSCOPYf_angle_d0.63820003
ELECTRON MICROSCOPYf_dihedral_angle_d6.1032000
ELECTRON MICROSCOPYf_chiral_restr0.0412338
ELECTRON MICROSCOPYf_plane_restr0.0042579

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