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- EMDB-73568: Structure of the 3-methylcrotonyl-coenzyme A carboxylase from Myc... -

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Basic information

Entry
Database: EMDB / ID: EMD-73568
TitleStructure of the 3-methylcrotonyl-coenzyme A carboxylase from Mycobacterium smegmatis
Map dataUnsharpened map
Sample
  • Complex: 3-methylcrotonyl-coenzyme A carboxylase from Mycobacterium smegmatis
    • Protein or peptide: Carboxyl transferase domain protein
    • Protein or peptide: biotin carboxylase
  • Ligand: BIOTIN
KeywordsCarboxylase / transferase / leucine catabolism / metabolism / LIGASE
Function / homology
Function and homology information


methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / L-leucine catabolic process / biotin carboxylase / biotin carboxylase activity / transferase activity / ATP binding / metal ion binding
Similarity search - Function
: / Methylcrotonyl-CoA carboxylase, alpha-subunit, BT domain / 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 ...: / Methylcrotonyl-CoA carboxylase, alpha-subunit, BT domain / 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
biotin carboxylase / Carboxyl transferase domain protein
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsLiang Y / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT191893 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural basis for substrate specificity and MSMEG_0435-0436 binding by the mycobacterial long-chain acyl-CoA carboxylase complex.
Authors: Yingke Liang / Stephanie A Bueler / John L Rubinstein /
Abstract: The presence of mycolic acid is a defining feature of the mycobacterial cell wall, which provides a highly impermeable barrier to many antibiotics. Biosynthesis of this fatty acid, as well as ...The presence of mycolic acid is a defining feature of the mycobacterial cell wall, which provides a highly impermeable barrier to many antibiotics. Biosynthesis of this fatty acid, as well as tuberculostearic acid, requires precursor molecules produced by the essential long-chain acyl-coenzyme A (CoA) carboxylase (LCC) complex. The LCC complex catalyzes carboxylation of the α-carbon of long-chain acyl-CoA, but also short-chain acetyl-CoA and propionyl-CoA. The complex includes the subunits AccA3, which contains a biotin carboxylase (BC) domain and a biotin carboxyl carrier protein (BCCP) domain, the long-chain acyl-CoA carboxyltransferase AccD4, the short-chain acyl-CoA carboxyltransferase AccD5, and the incompletely characterized protein AccE. We used electron cryomicroscopy (cryo-EM) to determine structures of the LCC complex from . In the structures, two AccE subunits tether eight AccA3 subunits to an AccD4AccD5 heterohexamer core. Cryo-EM of the enzyme during catalysis reveals how AccD4 and AccD5 achieve substrate specificity, with AccD5 binding tightly to CoA and AccD4 binding long acyl chains. The BCCP domains of AccA3 undergo long-distance translocation to transfer a carboxyl group from the BC domain of AccA3 to the acyl-CoA substrate bound in AccD5. Further, we find that two copies of a protein complex formed from MSMEG_0435 and MSMEG_0436 can bind the LCC complex, sequestering the biotin moiety of BCCP domains near AccD5 and decreasing propionyl-CoA carboxylase activity. Rv0263c, the ortholog of MSMEG_0435, has a role in bacterial survival during transmission, suggesting that these proteins may regulate production of branched fatty acid precursors for the mycobacterial cell wall.
History
DepositionOct 26, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73568.png

Downloads & links

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Map

FileDownload / File: emd_73568.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 480 pix.
= 446.4 Å		0.93 Å/pix.
x 480 pix.
= 446.4 Å		0.93 Å/pix.
x 480 pix.
= 446.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.54072547 - 1.2587034
Average (Standard dev.)-0.00060257665 (±0.03148702)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 446.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_73568_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73568_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73568_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : 3-methylcrotonyl-coenzyme A carboxylase from Mycobacterium smegmatis

EntireName: 3-methylcrotonyl-coenzyme A carboxylase from Mycobacterium smegmatis
Components
  • Complex: 3-methylcrotonyl-coenzyme A carboxylase from Mycobacterium smegmatis
    • Protein or peptide: Carboxyl transferase domain protein
    • Protein or peptide: biotin carboxylase
  • Ligand: BIOTIN

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Supramolecule #1: 3-methylcrotonyl-coenzyme A carboxylase from Mycobacterium smegmatis

SupramoleculeName: 3-methylcrotonyl-coenzyme A carboxylase from Mycobacterium smegmatis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 750 KDa

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Macromolecule #1: Carboxyl transferase domain protein

MacromoleculeName: Carboxyl transferase domain protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 54.816199 KDa
SequenceString: MSSHRDEHLA LVAELRSKLA AAALGGPERA RERHVGRGKL LPRDRVDGLL DPGSPFLELA PLAAGGMYDD ECPGAGMIAG IGRVSGREC VIVANDATVK GGTYYPITVK KHLRAQEIAL QNKLPCIYLV DSGGAFLPRQ DEVFPDRDHF GRIFYNQATM S AQGIAQIA ...String:
MSSHRDEHLA LVAELRSKLA AAALGGPERA RERHVGRGKL LPRDRVDGLL DPGSPFLELA PLAAGGMYDD ECPGAGMIAG IGRVSGREC VIVANDATVK GGTYYPITVK KHLRAQEIAL QNKLPCIYLV DSGGAFLPRQ DEVFPDRDHF GRIFYNQATM S AQGIAQIA AVLGSCTAGG AYVPAMSDEA VIVRNQGTIF LGGPPLVKAA TGEVVTAEEL GGGDLHSKTS GVTDHLAHDD RD ALRIVRN IVATLGPAEP PPWQVLPAVD PIADQTELYD VVPVDARVPY DVHEVITRIV DGGEFGEFKA EYGTTLVTGF ARI HGHPVG IIANNGVLFG ESAVKGAHFI ELCDKRKTPL LFLQNISGFM VGRDYEAGGI AKHGAKMVTA VACARVPKLT VVIG GSYGA GNYSMCGRAY SPRFLWMWPN ARISVMGGEQ AASVLATVRG EMTDAEAEEF KAPIREQYEH QGNPYYSTAR LWDDG VIDP ADTRTVVGLA LSVVGQAPLE PVSYGVFRM

UniProtKB: Carboxyl transferase domain protein

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Macromolecule #2: biotin carboxylase

MacromoleculeName: biotin carboxylase / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO / EC number: biotin carboxylase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 70.144711 KDa
SequenceString: MMMSSQTFDT VLVANRGEIA VRVIRTLRAM GIRSVAVFSE ADAGARHVTE ADVAVCIGPA AARHSYLDID AVVGAARRTD AQAVHPGYG FLSENAEFAS ALATAGIVFI GPPASAIATM GDKIAAKAAV SAFGVPVVPG ISRPGLADDD LIAGAAEVGY P VLVKPSAG ...String:
MMMSSQTFDT VLVANRGEIA VRVIRTLRAM GIRSVAVFSE ADAGARHVTE ADVAVCIGPA AARHSYLDID AVVGAARRTD AQAVHPGYG FLSENAEFAS ALATAGIVFI GPPASAIATM GDKIAAKAAV SAFGVPVVPG ISRPGLADDD LIAGAAEVGY P VLVKPSAG GGGKGMRVVE AAADLPAALV SARREAGAAF GDDTLFLERF VQRPRHIEVQ VLADGHGNVI HLGERECSLQ RR HQKVIEE APSPLLDEAT RARIGAAACA TARSVDYTGA GTVEFIVSAD RPDEFFFMEM NTRLQVEHPV TELVTGIDLV EQQ IRIAAG EPLAIGQDDI TLTGHAVEAR VYAEDPAAGF LPTGGDVLGL REPTGRGVRV DSGLAAGTVV GSDYDPMLSK IIAH GSDRA SALQILDRAL ADTAVLGVTT NIEFLRFLLA DDDVAAGRLD TGLLDRRAPD FAPATVGDEQ LIAAAAYLWA RQWSA AGGD LWRVPSGWRV GEWAPATFRL HAGDRTDHVY ITGNPERASA AVEHGDTHTV SADFTPGSDT FAVTLDGLRT DYRVAV TDS QIWLSGGGRT WSVQKVREEP VRPDDAHSGD AELVSPMPGS VVAVGVPDGS DVTAGTVVVT VEAMKMEHAL TAPVDGV AK ILVAVGDQVK VGQPLARITA HTQENES

UniProtKB: biotin carboxylase

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Macromolecule #3: BIOTIN

MacromoleculeName: BIOTIN / type: ligand / ID: 3 / Number of copies: 6 / Formula: BTN
Molecular weightTheoretical: 244.311 Da
Chemical component information

ChemComp-BTN:
BIOTIN

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 6
GridModel: Homemade / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 35 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 8000 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 20.0 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 5.0.0-privatebeta) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: Initial model was generated ab initio in cryoSPARC v5.0.0-privatebeta
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.0-privatebeta) / Number images used: 30234
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.0-privatebeta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.0-privatebeta)
FSC plot (resolution estimation)

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