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- PDB-8f3d: 3-methylcrotonyl-CoA carboxylase in filament, beta-subunit centered -

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Basic information

Entry
Database: PDB / ID: 8f3d
Title3-methylcrotonyl-CoA carboxylase in filament, beta-subunit centered
Components
  • 3-methylcrotonyl-CoA carboxylase alpha-subunit
  • 3-methylcrotonyl-CoA carboxylase beta-subunit
KeywordsLIGASE / enzyme / multienzyme / multi-enzyme / biotin-dependent / leucine catabolism / PROTEIN FIBRIL
Function / homology
Function and homology information


urea carboxylase activity / methylcrotonoyl-CoA carboxylase activity / propionyl-CoA carboxylase activity / mitochondrion / ATP binding / membrane / metal ion binding
Similarity search - Function
Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain ...Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Chem-BTI / Methylcrotonoyl-coa carboxylase biotinylated subunitprotein-like protein
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHu, J.J. / Lee, J.K.J. / Liu, Y.T. / Yu, C. / Huang, L. / Afasizheva, I. / Afasizhev, R. / Zhou, Z.H.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI101057 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM074830 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR23057 United States
National Institutes of Health/Office of the DirectorS10OD018111 United States
National Science Foundation (NSF, United States)DBI-133813 United States
Citation
Journal: Structure / Year: 2023
Title: Discovery, structure, and function of filamentous 3-methylcrotonyl-CoA carboxylase.
Authors: Jason J Hu / Jane K J Lee / Yun-Tao Liu / Clinton Yu / Lan Huang / Inna Aphasizheva / Ruslan Aphasizhev / Z Hong Zhou /
Abstract: 3-methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent mitochondrial enzyme necessary for leucine catabolism in most organisms. While the crystal structure of recombinant bacterial MCC has been ...3-methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent mitochondrial enzyme necessary for leucine catabolism in most organisms. While the crystal structure of recombinant bacterial MCC has been characterized, the structure and potential polymerization of native MCC remain elusive. Here, we discovered that native MCC from Leishmania tarentolae (LtMCC) forms filaments, and determined the structures of different filament regions at 3.4, 3.9, and 7.3 Å resolution using cryoEM. αβ LtMCCs assemble in a twisted-stacks architecture, manifesting as supramolecular rods up to 400 nm. Filamentous LtMCCs bind biotin non-covalently and lack coenzyme A. Filaments elongate by stacking αβ LtMCCs onto the exterior α-trimer of the terminal LtMCC. This stacking immobilizes the biotin carboxylase domains, sequestering the enzyme in an inactive state. Our results support a new model for LtMCC catalysis, termed the dual-swinging-domains model, and cast new light on the function of polymerization in the carboxylase superfamily and beyond.
#1: Journal: To Be Published
Title: Discovery, Structure, and Function of Filamentous 3-Methylcrotonyl-CoA Carboxylase
Authors: Hu, J.J. / Lee, J.K.J. / Liu, Y.T. / Yu, C. / Huang, L. / Afasizheva, I. / Afasizhev, R. / Zhou, Z.H.
History
DepositionNov 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-methylcrotonyl-CoA carboxylase beta-subunit
B: 3-methylcrotonyl-CoA carboxylase beta-subunit
C: 3-methylcrotonyl-CoA carboxylase beta-subunit
D: 3-methylcrotonyl-CoA carboxylase beta-subunit
E: 3-methylcrotonyl-CoA carboxylase beta-subunit
F: 3-methylcrotonyl-CoA carboxylase beta-subunit
H: 3-methylcrotonyl-CoA carboxylase alpha-subunit
I: 3-methylcrotonyl-CoA carboxylase alpha-subunit
J: 3-methylcrotonyl-CoA carboxylase alpha-subunit
K: 3-methylcrotonyl-CoA carboxylase alpha-subunit
L: 3-methylcrotonyl-CoA carboxylase alpha-subunit
M: 3-methylcrotonyl-CoA carboxylase alpha-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)917,87918
Polymers916,50912
Non-polymers1,3706
Water00
1


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

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Components

#1: Protein
3-methylcrotonyl-CoA carboxylase beta-subunit


Mass: 76468.469 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: TATII/UC / References: methylcrotonoyl-CoA carboxylase
#2: Protein
3-methylcrotonyl-CoA carboxylase alpha-subunit


Mass: 76283.070 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Strain: TATII/UC / References: UniProt: A0A640KPA4
#3: Chemical
ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N2O2S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA filament
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: TATII/UC
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13250 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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