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- PDB-9tqg: L. pneumophila 3-methylcrotonyl-CoA carboxylase A1B6 -

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Basic information

Entry
Database: PDB / ID: 9tqg
TitleL. pneumophila 3-methylcrotonyl-CoA carboxylase A1B6
Components
  • Biotin carboxylase
  • Propionyl CoA carboxylase beta subunit
KeywordsLIGASE / 3-methylcrotonyl-CoA carboxylase / biotin
Function / homology
Function and homology information


methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / propionyl-CoA carboxylase / L-leucine catabolic process / propionyl-CoA carboxylase activity / ligase activity / ATP binding / metal ion binding
Similarity search - Function
Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-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, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-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 synthase subdomain signature 1. / 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 / Biotin carboxylase / Propionyl CoA carboxylase beta subunit
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsMeir, A. / Durie, C. / Somarathne, R. / Shrestha, R. / Zehra, M. / Brodeur, C. / Bhella, D. / Lai, W.C.
Funding support United States, United Kingdom, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM150663 United States
Medical Research Council (MRC, United Kingdom)MC_UU_00034/1 United Kingdom
CitationJournal: bioRxiv / Year: 2025
Title: Substrate-enhanced filamentation of 3-methylcrotonyl-CoA carboxylase in .
Authors: Radha P Somarathne / Riti Shrestha / Mishghan Zehra / Cole Brodeur / David Bhella / Wing-Cheung Lai / Amit Meir / Clarissa L Durie
Abstract: 3-Methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent carboxylase that metabolizes the amino acid leucine. MCC is present in bacteria, fungi, plants, and animals. In humans, its overexpression ...3-Methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent carboxylase that metabolizes the amino acid leucine. MCC is present in bacteria, fungi, plants, and animals. In humans, its overexpression is linked to cancer, and its deficiency is linked to inborn errors of metabolism with severe consequences, so understanding its structure and function has far reaching implications. Here, we explore the MCC from , a pathogenic bacterium with a biphasic life cycle. Our endogenous holoenzyme yielded the highest resolution cryo-EM structure of MCC to date, allowing for identification of protein components by the machine learning tool ModelAngelo, confirmed independently by mass spectrometry. We also observed, for the first time, enhanced filamentation of MCC upon substrate binding. We propose that this filamentation, previously observed in the eukaryotes, but not in bacteria, may be important for cellular processes such as differentiation of life cycle or cell division.
History
DepositionDec 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.1Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Propionyl CoA carboxylase beta subunit
B: Propionyl CoA carboxylase beta subunit
C: Propionyl CoA carboxylase beta subunit
D: Propionyl CoA carboxylase beta subunit
E: Propionyl CoA carboxylase beta subunit
F: Propionyl CoA carboxylase beta subunit
L: Biotin carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)427,65010
Polymers426,9657
Non-polymers6853
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
Propionyl CoA carboxylase beta subunit


Mass: 58525.625 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: lpg1827 / Source: (natural) Legionella pneumophila (bacteria) / Strain: Phildelphia 1 / References: UniProt: Q5ZUH1, propionyl-CoA carboxylase
#2: Protein Biotin carboxylase / Acetyl-coenzyme A carboxylase biotin carboxylase subunit A


Mass: 75810.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: lpg 1829 / Source: (natural) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / References: UniProt: A0AAN5PJF4
#3: Chemical ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N2O2S / Feature type: SUBJECT OF INVESTIGATION
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: L. pneumophila 3-methylcrotonyl-CoA carboxylase / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 365 kDa/nm / Experimental value: YES
Source (natural)Organism: Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / Cellular location: Cytoplasm
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.22 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 31641
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
3EPUimage acquisitionEPU was used for data collection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1504197
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78376 / Symmetry type: POINT
RefinementHighest resolution: 2.68 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00226220
ELECTRON MICROSCOPYf_angle_d0.49335518
ELECTRON MICROSCOPYf_dihedral_angle_d5.2673660
ELECTRON MICROSCOPYf_chiral_restr0.0433930
ELECTRON MICROSCOPYf_plane_restr0.0044655

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