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- PDB-8jxm: Human 3-methylcrotonyl-CoA carboxylase in BCCP-H2 state with MCoA -

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Basic information

Entry
Database: PDB / ID: 8jxm
TitleHuman 3-methylcrotonyl-CoA carboxylase in BCCP-H2 state with MCoA
Components
  • Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
  • Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
KeywordsCYTOSOLIC PROTEIN / MCC / Mitochondrial
Function / homology
Function and homology information


3-Methylcrotonyl-CoA carboxylase deficiency / methylcrotonoyl-CoA carboxylase / biotin metabolic process / methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / L-leucine catabolic process / biotin carboxylase activity / branched-chain amino acid catabolic process ...3-Methylcrotonyl-CoA carboxylase deficiency / methylcrotonoyl-CoA carboxylase / biotin metabolic process / methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / L-leucine catabolic process / biotin carboxylase activity / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / coenzyme A metabolic process / biotin binding / mitochondrial matrix / mitochondrion / ATP binding / metal ion binding / cytosol
Similarity search - Function
Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like / : / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin-binding site / Biotin-requiring enzymes attachment site. ...Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like / : / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Chem-BTI / : / Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial / Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsLiu, D.S. / Su, J.Y. / Tian, X.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071192 China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural insight into synergistic activation of human 3-methylcrotonyl-CoA carboxylase.
Authors: Jiayue Su / Xuyang Tian / Hang Cheng / Desheng Liu / Ziyi Wang / Shan Sun / Hong-Wei Wang / Sen-Fang Sui /
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 ...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.
History
DepositionJun 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 5, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
L: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
A: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
B: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
C: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
F: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
G: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
H: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
I: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
M: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
E: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
J: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)858,40824
Polymers851,94012
Non-polymers6,46812
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial / MCCase subunit beta / 3-methylcrotonyl-CoA carboxylase 2 / 3-methylcrotonyl-CoA carboxylase non- ...MCCase subunit beta / 3-methylcrotonyl-CoA carboxylase 2 / 3-methylcrotonyl-CoA carboxylase non-biotin-containing subunit / 3-methylcrotonyl-CoA:carbon dioxide ligase subunit beta


Mass: 61406.027 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCCC2, MCCB / Production host: Homo sapiens (human)
References: UniProt: Q9HCC0, methylcrotonoyl-CoA carboxylase
#2: Protein
Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial / MCCase subunit alpha / 3-methylcrotonyl-CoA carboxylase 1 / 3-methylcrotonyl-CoA carboxylase biotin- ...MCCase subunit alpha / 3-methylcrotonyl-CoA carboxylase 1 / 3-methylcrotonyl-CoA carboxylase biotin-containing subunit / 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha


Mass: 80584.016 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCCC1, MCCA / Production host: Homo sapiens (human)
References: UniProt: Q96RQ3, methylcrotonoyl-CoA carboxylase
#3: Chemical
ChemComp-TW3 / ~{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


Mass: 849.635 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C26H42N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N2O2S
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dodecamer of human MCC / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44531 / Symmetry type: POINT

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