8JXM

Human 3-methylcrotonyl-CoA carboxylase in BCCP-H2 state with MCoA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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
Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial563Homo sapiensMutation(s): 0 
Gene Names: MCCC2MCCB
EC: 6.4.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCC0 (Homo sapiens)
Explore Q9HCC0 
Go to UniProtKB:  Q9HCC0
PHAROS:  Q9HCC0
GTEx:  ENSG00000131844 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HCC0
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 subunit alpha, mitochondrial725Homo sapiensMutation(s): 0 
Gene Names: MCCC1MCCA
EC: 6.4.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RQ3 (Homo sapiens)
Explore Q96RQ3 
Go to UniProtKB:  Q96RQ3
PHAROS:  Q96RQ3
GTEx:  ENSG00000078070 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RQ3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TW3 (Subject of Investigation/LOI)
Query on TW3

Download Ideal Coordinates CCD File 
M [auth K]
N [auth A]
P [auth C]
T [auth H]
W [auth E]
M [auth K],
N [auth A],
P [auth C],
T [auth H],
W [auth E],
X [auth J]
~{S}-[2-[3-[[(2~{R})-4-[[[(2~{S},3~{S},4~{S},5~{S})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-methylbut-2-enethioate
C26 H42 N7 O17 P3 S
BXIPALATIYNHJN-XDPCYSMHSA-N
BTI
Query on BTI

Download Ideal Coordinates CCD File 
O [auth C]
Q [auth F]
R [auth G]
S [auth H]
U [auth I]
O [auth C],
Q [auth F],
R [auth G],
S [auth H],
U [auth I],
V [auth M]
5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
C10 H16 N2 O2 S
ARDNWGMSCXSPBF-CIUDSAMLSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 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)China32071192

Revision History  (Full details and data files)

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