8F3D

3-methylcrotonyl-CoA carboxylase in filament, beta-subunit centered

  • Classification: LIGASE
  • Organism(s): Leishmania tarentolae
  • Mutation(s): No 

  • Deposited: 2022-11-09 Released: 2023-01-11 
  • Deposition Author(s): Hu, J.J., Lee, J.K.J., Liu, Y.T., Yu, C., Huang, L., Afasizheva, I., Afasizhev, R., Zhou, Z.H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Science Foundation (NSF, United States), National Institutes of Health/National Center for Research Resources (NIH/NCRR), National Institutes of Health/Office of the Director

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery, structure, and function of filamentous 3-methylcrotonyl-CoA carboxylase.

Hu, J.J.Lee, J.K.J.Liu, Y.T.Yu, C.Huang, L.Aphasizheva, I.Aphasizhev, R.Zhou, Z.H.

(2023) Structure 31: 100-110.e4

  • DOI: https://doi.org/10.1016/j.str.2022.11.015
  • Primary Citation of Related Structures:  
    8F3D, 8F41

  • PubMed 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 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. α 6 β 6 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 α 6 β 6 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.


  • Organizational Affiliation

    Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA; Department of Mathematics, UCLA, Los Angeles, CA 90095, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-methylcrotonyl-CoA carboxylase beta-subunit
A, B, C, D, E
A, B, C, D, E, F
707Leishmania tarentolaeMutation(s): 0 
EC: 6.4.1.4
UniProt
Find proteins for A0A640KGP9 (Leishmania tarentolae)
Explore A0A640KGP9 
Go to UniProtKB:  A0A640KGP9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A640KGP9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
3-methylcrotonyl-CoA carboxylase alpha-subunit687Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KPA4 (Leishmania tarentolae)
Explore A0A640KPA4 
Go to UniProtKB:  A0A640KPA4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A640KPA4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM071940
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI101057
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM074830
National Science Foundation (NSF, United States)United StatesDMR-1548924
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10RR23057
National Institutes of Health/Office of the DirectorUnited StatesS10OD018111
National Science Foundation (NSF, United States)United StatesDBI-133813

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-01-18
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection