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- EMDB-40473: Leishmania tarentolae propionyl-CoA carboxylase (alpha-5-beta-6) -

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Basic information

Entry
Database: EMDB / ID: EMD-40473
TitleLeishmania tarentolae propionyl-CoA carboxylase (alpha-5-beta-6)
Map dataLeishmania tarentolae propionyl-CoA carboxylase (alpha-5-beta-6)
Sample
  • Complex: Leishmania tarentolae propionyl-CoA carboxylase
    • Protein or peptide: propionyl-CoA carboxylase
    • Protein or peptide: Propionyl-coa carboxylase beta chain, putative
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
KeywordsMultienzyme complex / carboxylase / LIGASE
Function / homology
Function and homology information


propionyl-CoA carboxylase / propionyl-CoA carboxylase activity / lipid catabolic process / mitochondrion / ATP binding / metal ion binding
Similarity search - Function
Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT domain / : / : / 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 ...Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT domain / : / : / 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 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
propionyl-CoA carboxylase / Propionyl-CoA carboxylase beta chain, mitochondrial
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.62 Å
AuthorsLee JKJ / Liu YT / Hu JJ / Aphasizheva I / Aphasizhev R / Zhou ZH
Funding support United States, 2 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
CitationJournal: J Struct Biol X / Year: 2023
Title: CryoEM reveals oligomeric isomers of a multienzyme complex and assembly mechanics.
Authors: Jane K J Lee / Yun-Tao Liu / Jason J Hu / Inna Aphasizheva / Ruslan Aphasizhev / Z Hong Zhou /
Abstract: Propionyl-CoA carboxylase (PCC) is a multienzyme complex consisting of up to six α-subunits and six β-subunits. Belonging to a metabolic pathway converging on the citric acid cycle, it is present ...Propionyl-CoA carboxylase (PCC) is a multienzyme complex consisting of up to six α-subunits and six β-subunits. Belonging to a metabolic pathway converging on the citric acid cycle, it is present in most forms of life and irregularities in its assembly lead to serious illness in humans, known as propionic acidemia. Here, we report the cryogenic electron microscopy (cryoEM) structures and assembly of different oligomeric isomers of endogenous PCC from the parasitic protozoan (LtPCC). These structures and their statistical distribution reveal the mechanics of PCC assembly and disassembly at equilibrium. We show that, in solution, endogenous LtPCC β-subunits form stable homohexamers, to which different numbers of α-subunits attach. Sorting LtPCC particles into seven classes (i.e., oligomeric formulae αβ, αβ, αβ, αβ, αβ, αβ, αβ) enables formulation of a model for PCC assembly. Our results suggest how multimerization regulates PCC enzymatic activity and showcase the utility of cryoEM in revealing the statistical mechanics of reaction pathways.
History
DepositionApr 13, 2023-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40473.png

Downloads & links

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Map

FileDownload / File: emd_40473.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLeishmania tarentolae propionyl-CoA carboxylase (alpha-5-beta-6)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0105
Minimum - Maximum-0.015206444 - 0.03231608
Average (Standard dev.)0.00014176453 (±0.0016990264)
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: Half Map 1

Fileemd_40473_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_40473_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Leishmania tarentolae propionyl-CoA carboxylase

EntireName: Leishmania tarentolae propionyl-CoA carboxylase
Components
  • Complex: Leishmania tarentolae propionyl-CoA carboxylase
    • Protein or peptide: propionyl-CoA carboxylase
    • Protein or peptide: Propionyl-coa carboxylase beta chain, putative
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL

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Supramolecule #1: Leishmania tarentolae propionyl-CoA carboxylase

SupramoleculeName: Leishmania tarentolae propionyl-CoA carboxylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Leishmania tarentolae (eukaryote)

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Macromolecule #1: propionyl-CoA carboxylase

MacromoleculeName: propionyl-CoA carboxylase / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 73.277656 KDa
SequenceString: VLVANRGEIA CRVMATCRRL GIKTVAVYST ADEQAKHVKV ADESVCIGPP ASVESYLCID KIVDACKKTG AQAVHPGYGF LSENGEFQS ALQKNNIVFV GPDAHSIESM GDKIESKRLA QRAGVTCIPG FIGEVKTHED LLRFAREIGY PVMIKASGGG G GKGMRVAY ...String:
VLVANRGEIA CRVMATCRRL GIKTVAVYST ADEQAKHVKV ADESVCIGPP ASVESYLCID KIVDACKKTG AQAVHPGYGF LSENGEFQS ALQKNNIVFV GPDAHSIESM GDKIESKRLA QRAGVTCIPG FIGEVKTHED LLRFAREIGY PVMIKASGGG G GKGMRVAY NDTQCVEYYD MCREEAKAAF HSDKMLVERF IDHPRHIEIQ VIADRRGNTV YLPERECSIQ RRNQKVIEEA PS VLLDATT RKAMGEEAVA MARAVQYVSA GTVENVVNPQ KQFYFLEMNT RLQVEHPITE EITGVDLVEQ MLRAAADLPL SIT QDDITI NGHATECRVY AEDPMKNYFP SIGRLTMYQE PTGAGVRCDS GIIEGSQISV YYDPLICKLS TWGRDRAECI GRME KALDE YVIRGLRHNI CLLRDVVTEP RYRSGSITTN YLQEQYPNGF KKAELTAEEM QLMYEVAACV HLKRERLHYT QGTAP SERQ LYLSVGAGQE GETPVYVRYL DDSHFEIGAS KHGPFRKMEV VWKASYPIIR VKDGEAETVL QFWGTNEVTY GMQMRG TTF DVNVMSDLQS TLAHFVPITE ATTNTKQILS PMPGVIVAIK VQPGQMVVAG EELLTLEAMK MRNKIHAQAD GKVKEVK VK LGATVEDNEV LVELE

UniProtKB: propionyl-CoA carboxylase

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Macromolecule #2: Propionyl-coa carboxylase beta chain, putative

MacromoleculeName: Propionyl-coa carboxylase beta chain, putative / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 53.587285 KDa
SequenceString: PTAAEDLRHK KKRLTAMERV QLFCDPGTFR ERDALVEHEC HNFGMEKRKV PGDGFITGTG KVFGRPVFLF SHDFTVFGGS LSRTNAAKV VRIMEEAAKI GVPVIGFNDS GGARIHEGVD SLAGYADIFL RNTLFSGVIP QISVIMGPCA GGAVYSPAIT D FTFMVETS ...String:
PTAAEDLRHK KKRLTAMERV QLFCDPGTFR ERDALVEHEC HNFGMEKRKV PGDGFITGTG KVFGRPVFLF SHDFTVFGGS LSRTNAAKV VRIMEEAAKI GVPVIGFNDS GGARIHEGVD SLAGYADIFL RNTLFSGVIP QISVIMGPCA GGAVYSPAIT D FTFMVETS SYMFVTGPEV VSAVGGKLVT KDELGGPHVH ATKSGVSAGT FPNDIVAMAQ LRRLYSYLPL SNRDPVPVLP TA DERYRDV SSLNTVVPTE VKEAYDMRDV IYPVIDHDSF FEIQPQFAKN IICGFARVEG RSVCIIANQP KVQAGVLDID SSV KGARMV RFADAFNIPI ITFVDVPGFL PGVQQEYGGI IRHGAKLLYA YAEATVPKVT IITRKAYGGA YDVMSSKHLR GDSN YAWPH AEIAVMGAAG ACKLLYSKET AEQQAQRIAD YEKTFCTPLS AARKGFVDAV IDPSETRMRV CEDLERLARK QLQNP WKKH GNIPL

UniProtKB: Propionyl-CoA carboxylase beta chain, mitochondrial

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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 stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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: 8.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16034
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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