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- EMDB-28849: 3-methylcrotonyl-CoA carboxylase in filament, alpha-subunit centered -

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Basic information

Entry
Database: EMDB / ID: EMD-28849
Title3-methylcrotonyl-CoA carboxylase in filament, alpha-subunit centered
Map datamcc
Sample
  • Complex: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA carboxylase filament
    • Protein or peptide: 3-methylcrotonyl-CoA carboxylase, beta-subunit
    • Protein or peptide: 3-methylcrotonyl-CoA carboxylase, alpha-subunit
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
Keywordsenzyme / multienzyme / multi-enzyme / biotin-dependent / leucine catabolism / PROTEIN FIBRIL / LIGASE
Function / homology
Function and homology information


urea carboxylase activity / methylcrotonoyl-CoA carboxylase activity / propionyl-CoA carboxylase activity / mitochondrion / ATP binding / membrane / metal ion binding
Similarity search - Function
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 ...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. / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Methylcrotonoyl-coa carboxylase biotinylated subunitprotein-like protein
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHu JJ / Lee JKJ / Liu YT / Yu C / Huang L / Afasizheva I / Afasizhev R / Zhou ZH
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI101057 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM074830 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR23057 United States
National Institutes of Health/Office of the DirectorS10OD018111 United States
National Science Foundation (NSF, United States)DBI-133813 United States
CitationJournal: Structure / Year: 2023
Title: Discovery, structure, and function of filamentous 3-methylcrotonyl-CoA carboxylase.
Authors: Jason J Hu / Jane K J Lee / Yun-Tao Liu / Clinton Yu / Lan Huang / Inna Aphasizheva / Ruslan Aphasizhev / Z Hong Zhou /
Abstract: 3-methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent mitochondrial enzyme necessary for leucine catabolism in most organisms. While the crystal structure of recombinant bacterial MCC has been ...3-methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent mitochondrial enzyme necessary for leucine catabolism in most organisms. While the crystal structure of recombinant bacterial MCC has been characterized, the structure and potential polymerization of native MCC remain elusive. Here, we discovered that native MCC from Leishmania tarentolae (LtMCC) forms filaments, and determined the structures of different filament regions at 3.4, 3.9, and 7.3 Å resolution using cryoEM. αβ LtMCCs assemble in a twisted-stacks architecture, manifesting as supramolecular rods up to 400 nm. Filamentous LtMCCs bind biotin non-covalently and lack coenzyme A. Filaments elongate by stacking αβ LtMCCs onto the exterior α-trimer of the terminal LtMCC. This stacking immobilizes the biotin carboxylase domains, sequestering the enzyme in an inactive state. Our results support a new model for LtMCC catalysis, termed the dual-swinging-domains model, and cast new light on the function of polymerization in the carboxylase superfamily and beyond.
History
DepositionNov 10, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28849.png

Downloads & links

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Map

FileDownload / File: emd_28849.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmcc
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.048353195 - 0.084034376
Average (Standard dev.)0.00019211888 (±0.0042585614)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: h2

Fileemd_28849_half_map_1.map
Annotationh2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: h1

Fileemd_28849_half_map_2.map
Annotationh1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : alpha6beta6 dodecamer in 3-methylcrotonyl-CoA carboxylase filament

EntireName: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA carboxylase filament
Components
  • Complex: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA carboxylase filament
    • Protein or peptide: 3-methylcrotonyl-CoA carboxylase, beta-subunit
    • Protein or peptide: 3-methylcrotonyl-CoA carboxylase, alpha-subunit
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL

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Supramolecule #1: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA carboxylase filament

SupramoleculeName: alpha6beta6 dodecamer in 3-methylcrotonyl-CoA carboxylase filament
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: TATII/UC

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Macromolecule #1: 3-methylcrotonyl-CoA carboxylase, beta-subunit

MacromoleculeName: 3-methylcrotonyl-CoA carboxylase, beta-subunit / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: methylcrotonoyl-CoA carboxylase
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: TATII/UC
Molecular weightTheoretical: 61.978711 KDa
SequenceString: YAHHPIDYER STSKSPNILR LPANTSDPTY QENMARMEGL VEQLRARVRY VQAGGVVPEE EAAKAGVSIS SIEADDRVRK LHLSRGKML ARDRIERLID PGTRFLELSQ LAGWDLYWDD KKKEYERCYS GGIVTGIGLV NGVRCMLVAN DATVKGGTYY P ITVKKHLR ...String:
YAHHPIDYER STSKSPNILR LPANTSDPTY QENMARMEGL VEQLRARVRY VQAGGVVPEE EAAKAGVSIS SIEADDRVRK LHLSRGKML ARDRIERLID PGTRFLELSQ LAGWDLYWDD KKKEYERCYS GGIVTGIGLV NGVRCMLVAN DATVKGGTYY P ITVKKHLR AQKIAEQNHL PCIYLVDSGG ANLSRQDDVF PDEQHFGRIF YNEAQMSIKS ISQIAVVMGS CTAGGAYVPA MA DENIIVA RNGTIFLGGP PLVLAATGEK VSSEELGGAD VHCRISGVGD HYATDDLHAL YLARRAVANL NLKEHNEARN PTD VKPVPP LYDPRELGGF IPDMLSDVVK SFDVRAIIAR IVDGSRFDEF KALYGNTLVC GFARIEGMQV GIIANQGILY SESA LKGAH FIGLCTQRNV PLLFLQNITG FMVGKKYEEG GIARNGARLV MAVSSAPVPK VTVLIGGSYG AGNYGMCGRA FEPRF LFMW PNARISVMGG TQAATVLTLT NRNLKNASEA EIAAFKDKVK KKYEKEGSCY YSTARLWDDG VIAPEDTRVV VAEALR ATR LAP

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Macromolecule #2: 3-methylcrotonyl-CoA carboxylase, alpha-subunit

MacromoleculeName: 3-methylcrotonyl-CoA carboxylase, alpha-subunit / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO / EC number: methylcrotonoyl-CoA carboxylase
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: TATII/UC
Molecular weightTheoretical: 75.103633 KDa
SequenceString: ERKVEKLLVA NRGEIACRVF RTCREMHIRT VALFCEAERN AKHVAEADEA VCIGPPPAVN SYLRGEHIIS VAKQLNVDAI HPGYGFLSE NASFADAITR SGIEFIGPPA SAISLMGSKS ESKRIMEAAG VPVVPGYYGE NQNVSFLAEE AKKVGFPILI K AVSGGGGK ...String:
ERKVEKLLVA NRGEIACRVF RTCREMHIRT VALFCEAERN AKHVAEADEA VCIGPPPAVN SYLRGEHIIS VAKQLNVDAI HPGYGFLSE NASFADAITR SGIEFIGPPA SAISLMGSKS ESKRIMEAAG VPVVPGYYGE NQNVSFLAEE AKKVGFPILI K AVSGGGGK GMKIVERPED FTFMLESAKR EATNFFKDDR VILERYVKRS RHIECQIFFD KHGRGVFFFE RDCSVQRRYQ KV LEEAPAP HLSMETRQRI GEVALQAAKA VGYVGAGTVE FIFDTSTGEF YFMEMNTRLQ VEHPVTEEVC RIKGAPLDLV KLQ IKTAMG KPLTFSQEDV TLVGSCIEAR VYAESPERGF LPESGPLTFI REPFQGVRGP ARTRLDTGFR EGDNVLIHYD PMLA KVISW GRSREEALRG LRQALGEYKV AGINTNIEFL KRCCETPEFA RGGVTTNFIS EHESQLLKSP VVTPEVAAMA ATAWL LNRC DNWRGAFRLN SDTNATVHFY IDDHPVEVRL HTEGANYHKI FFSVWDHDGS FEVCSGPVTS KHRDQKSIVN DFTFLF ENG MHHTVLAVAT EGDVTVIGSF GLHQLRLLPL TDGFGDSSTA GGTSTKIVSP MPGKVSKLLV KSGDLVEKGQ VLVIVEA MK MEHPVRALQD GRVSFLVKEG EVVGGDHVLA TVAEEE

UniProtKB: Methylcrotonoyl-coa carboxylase biotinylated subunitprotein-like protein

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

MacromoleculeName: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
type: ligand / ID: 3 / Number of copies: 6 / Formula: BTI
Molecular weightTheoretical: 228.311 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7582
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8f41:
3-methylcrotonyl-CoA carboxylase in filament, alpha-subunit centered

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