8RTH

Trypanosoma brucei 3-methylcrotonyl-CoA carboxylase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The cryo-EM structure of trypanosome 3-methylcrotonyl-CoA carboxylase provides mechanistic and dynamic insights into its enzymatic function.

Plaza-Pegueroles, A.Aphasizheva, I.Aphasizhev, R.Fernandez-Tornero, C.Ruiz, F.M.

(2024) Structure 

  • DOI: https://doi.org/10.1016/j.str.2024.03.010
  • Primary Citation of Related Structures:  
    8RTH

  • PubMed Abstract: 

    3-Methylcrotonyl-CoA carboxylase (MCC) catalyzes the two-step, biotin-dependent production of 3-methylglutaconyl-CoA, an essential intermediate in leucine catabolism. Given the critical metabolic role of MCC, deficiencies in this enzyme lead to organic aciduria, while its overexpression is linked to tumor development. MCC is a dodecameric enzyme composed of six copies of each α- and β-subunit. We present the cryo-EM structure of the endogenous MCC holoenzyme from Trypanosoma brucei in a non-filamentous state at 2.4 Å resolution. Biotin is covalently bound to the biotin carboxyl carrier protein domain of α-subunits and positioned in a non-canonical pocket near the active site of neighboring β-subunit dimers. Moreover, flexibility of key residues at α-subunit interfaces and loops enables pivoting of α-subunit trimers to partly reduce the distance between α- and β-subunit active sites, required for MCC catalysis. Our results provide a structural framework to understand the enzymatic mechanism of eukaryotic MCCs and to assist drug discovery against trypanosome infections.


  • Organizational Affiliation

    Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, 28040 Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-methylcrotonyl-CoA carboxylase, putative
A, C, E, G, I
A, C, E, G, I, K
678Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q57YQ4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q57YQ4 
Go to UniProtKB:  Q57YQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57YQ4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
methylcrotonoyl-CoA carboxylase
B, D, F, H, J
B, D, F, H, J, L
612Trypanosoma bruceiMutation(s): 0 
EC: 6.4.1.4
UniProt
Find proteins for Q385A6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q385A6 
Go to UniProtKB:  Q385A6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ385A6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpain--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-04-24
    Changes: Database references