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Structure paper

TitleStructural insight into synergistic activation of human 3-methylcrotonyl-CoA carboxylase.
Journal, issue, pagesNat Struct Mol Biol, Year 2024
Publish dateSep 2, 2024
AuthorsJiayue Su / Xuyang Tian / Hang Cheng / Desheng Liu / Ziyi Wang / Shan Sun / Hong-Wei Wang / Sen-Fang Sui /
PubMed AbstractThe 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 ...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.
External linksNat Struct Mol Biol / PubMed:39223421
MethodsEM (single particle)
Resolution2.2 - 5.63 Å
Structure data

33729

7ybu

EMDB-33729, PDB-7ybu:
Human propionyl-coenzyme A carboxylase
Method: EM (single particle) / Resolution: 2.2 Å

35059

8hwl

EMDB-35059, PDB-8hwl:
Human Pyruvate Carboxylase
Method: EM (single particle) / Resolution: 5.63 Å

35980

8j4z

EMDB-35980, PDB-8j4z:
Human 3-methylcrotonyl-CoA carboxylase in BCCP-CTS state with substrate
Method: EM (single particle) / Resolution: 2.73 Å

36038

8j7d

EMDB-36038, PDB-8j7d:
Human 3-methylcrotonyl-CoA carboxylase in BCCP-H1 state
Method: EM (single particle) / Resolution: 2.7 Å

36044

8j7o

EMDB-36044, PDB-8j7o:
Human pyruvate carboxylase in BCCP-CTS state without BC
Method: EM (single particle) / Resolution: 3.83 Å

36136

8jaw

EMDB-36136, PDB-8jaw:
Human MCC in MCCD state
Method: EM (single particle) / Resolution: 2.51 Å

36705

8jxm

EMDB-36705, PDB-8jxm:
Human 3-methylcrotonyl-CoA carboxylase in BCCP-H2 state with MCoA
Method: EM (single particle) / Resolution: 3.49 Å

36706

8jxn

EMDB-36706, PDB-8jxn:
Human 3-methylcrotonyl-CoA carboxylase in BCCP-H1 state with MCoA
Method: EM (single particle) / Resolution: 3.2 Å

36840

8k2v

EMDB-36840, PDB-8k2v:
3-Methylcrotonyl-CoA Carboxylase in MCCD state with Acetyl CoA
Method: EM (single particle) / Resolution: 3.52 Å

Chemicals

ChemComp-BTI:
5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


ChemComp, No image

ChemComp-TW3:
Unknown entry

ChemComp-ACO:
ACETYL COENZYME *A

Source
  • homo sapiens (human)
KeywordsCYTOSOLIC PROTEIN / Cryo-EM / PCC / Mitochondria / PC / Mitochondrial / MCC / 3-methylcrotonyl-CoA / ACC / substrate

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