7YBU

Human propionyl-coenzyme A carboxylase

  • Classification: CYTOSOLIC PROTEIN
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2022-06-29 Released: 2023-07-05 
  • Deposition Author(s): Su, J.Y., Liu, D.S.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insight into synergistic activation of human 3-methylcrotonyl-CoA carboxylase.

Su, J.Tian, X.Cheng, H.Liu, D.Wang, Z.Sun, S.Wang, H.W.Sui, S.F.

(2024) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01379-3
  • Primary Citation of Related Structures:  
    7YBU, 8HWL, 8J4Z, 8J7D, 8J7O, 8JAW, 8JXM, 8JXN, 8K2V

  • PubMed Abstract: 

    The enzymes 3-methylcrotonyl-coenzyme A (CoA) carboxylase (MCC), pyruvate carboxylase and propionyl-CoA carboxylase belong to the biotin-dependent carboxylase family located in mitochondria. They participate in various metabolic pathways in human such as amino acid metabolism and tricarboxylic acid cycle. Many human diseases are caused by mutations in those enzymes but their structures have not been fully resolved so far. Here we report an optimized purification strategy to obtain high-resolution structures of intact human endogenous MCC, propionyl-CoA carboxylase and pyruvate carboxylase in different conformational states. We also determine the structures of MCC bound to different substrates. Analysis of MCC structures in different states reveals the mechanism of the substrate-induced, multi-element synergistic activation of MCC. These results provide important insights into the catalytic mechanism of the biotin-dependent carboxylase family and are of great value for the development of new drugs for the treatment of related diseases.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Propionyl-CoA carboxylase alpha chain, mitochondrial
A, B, D, F, H
A, B, D, F, H, J
728Homo sapiensMutation(s): 0 
EC: 6.4.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P05165 (Homo sapiens)
Explore P05165 
Go to UniProtKB:  P05165
PHAROS:  P05165
GTEx:  ENSG00000175198 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05165
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Propionyl-CoA carboxylase beta chain, mitochondrial
C,
E,
G,
I,
K,
L [auth P]
539Homo sapiensMutation(s): 0 
EC: 6.4.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P05166 (Homo sapiens)
Explore P05166 
Go to UniProtKB:  P05166
PHAROS:  P05166
GTEx:  ENSG00000114054 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05166
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31861143048

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Data collection
  • Version 1.2: 2024-11-27
    Changes: Data collection, Database references, Structure summary