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- EMDB-33729: Human propionyl-coenzyme A carboxylase -

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Basic information

Entry
Database: EMDB / ID: EMD-33729
TitleHuman propionyl-coenzyme A carboxylase
Map dataHuman propionyl-coenzyme A carboxylase
Sample
  • Complex: Human propionyl-coenzyme A carboxylase heterododecomer
    • Protein or peptide: Propionyl-CoA carboxylase alpha chain, mitochondrial
    • Protein or peptide: Propionyl-CoA carboxylase beta chain, mitochondrial
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
KeywordsCryo-EM / PCC / Mitochondria / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


short-chain fatty acid catabolic process / branched-chain amino acid metabolic process / Propionyl-CoA catabolism / propionyl-CoA carboxylase / propionyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / biotin binding / catalytic complex / Mitochondrial protein degradation ...short-chain fatty acid catabolic process / branched-chain amino acid metabolic process / Propionyl-CoA catabolism / propionyl-CoA carboxylase / propionyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / biotin binding / catalytic complex / Mitochondrial protein degradation / fatty acid metabolic process / mitochondrial matrix / enzyme binding / mitochondrion / ATP binding / metal ion binding / cytosol
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 / ATP-grasp fold, subdomain 1 / 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 alpha chain, mitochondrial / Propionyl-CoA carboxylase beta chain, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsSu JY / Liu DS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31861143048 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 29, 2022-
Header (metadata) releaseJul 5, 2023-
Map releaseJul 5, 2023-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33729.png

Downloads & links

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Map

FileDownload / File: emd_33729.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman propionyl-coenzyme A carboxylase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 360 pix.
= 389.7 Å		1.08 Å/pix.
x 360 pix.
= 389.7 Å		1.08 Å/pix.
x 360 pix.
= 389.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.131
Minimum - Maximum-0.61707044 - 1.8388704
Average (Standard dev.)-0.00036356444 (±0.05075462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 389.69998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Human propionyl-coenzyme A carboxylase half map A

Fileemd_33729_half_map_1.map
AnnotationHuman propionyl-coenzyme A carboxylase half map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Human propionyl-coenzyme A carboxylase half map B

Fileemd_33729_half_map_2.map
AnnotationHuman propionyl-coenzyme A carboxylase half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human propionyl-coenzyme A carboxylase heterododecomer

EntireName: Human propionyl-coenzyme A carboxylase heterododecomer
Components
  • Complex: Human propionyl-coenzyme A carboxylase heterododecomer
    • Protein or peptide: Propionyl-CoA carboxylase alpha chain, mitochondrial
    • Protein or peptide: Propionyl-CoA carboxylase beta chain, mitochondrial
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL

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Supramolecule #1: Human propionyl-coenzyme A carboxylase heterododecomer

SupramoleculeName: Human propionyl-coenzyme A carboxylase heterododecomer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Propionyl-CoA carboxylase alpha chain, mitochondrial

MacromoleculeName: Propionyl-CoA carboxylase alpha chain, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.161922 KDa
SequenceString: MAGFWVGTAP LVAAGRRGRW PPQQLMLSAA LRTLKHVLYY SRQCLMVSRN LGSVGYDPNE KTFDKILVAN RGEIACRVIR TCKKMGIKT VAIHSDVDAS SVHVKMADEA VCVGPAPTSK SYLNMDAIME AIKKTRAQAV HPGYGFLSEN KEFARCLAAE D VVFIGPDT ...String:
MAGFWVGTAP LVAAGRRGRW PPQQLMLSAA LRTLKHVLYY SRQCLMVSRN LGSVGYDPNE KTFDKILVAN RGEIACRVIR TCKKMGIKT VAIHSDVDAS SVHVKMADEA VCVGPAPTSK SYLNMDAIME AIKKTRAQAV HPGYGFLSEN KEFARCLAAE D VVFIGPDT HAIQAMGDKI ESKLLAKKAE VNTIPGFDGV VKDAEEAVRI AREIGYPVMI KASAGGGGKG MRIAWDDEET RD GFRLSSQ EAASSFGDDR LLIEKFIDNP RHIEIQVLGD KHGNALWLNE RECSIQRRNQ KVVEEAPSIF LDAETRRAMG EQA VALARA VKYSSAGTVE FLVDSKKNFY FLEMNTRLQV EHPVTECITG LDLVQEMIRV AKGYPLRHKQ ADIRINGWAV ECRV YAEDP YKSFGLPSIG RLSQYQEPLH LPGVRVDSGI QPGSDISIYY DPMISKLITY GSDRTEALKR MADALDNYVI RGVTH NIAL LREVIINSRF VKGDISTKFL SDVYPDGFKG HMLTKSEKNQ LLAIASSLFV AFQLRAQHFQ ENSRMPVIKP DIANWE LSV KLHDKVHTVV ASNNGSVFSV EVDGSKLNVT STWNLASPLL SVSVDGTQRT VQCLSREAGG NMSIQFLGTV YKVNILT RL AAELNKFMLE KVTEDTSSVL RSPMPGVVVA VSVKPGDAVA EGQEICVIEA MKMQNSMTAG KTGTVKSVHC QAGDTVGE G DLLVELE

UniProtKB: Propionyl-CoA carboxylase alpha chain, mitochondrial

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Macromolecule #2: Propionyl-CoA carboxylase beta chain, mitochondrial

MacromoleculeName: Propionyl-CoA carboxylase beta chain, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.284488 KDa
SequenceString: MAAALRVAAV GARLSVLASG LRAAVRSLCS QATSVNERIE NKRRTALLGG GQRRIDAQHK RGKLTARERI SLLLDPGSFV ESDMFVEHR CADFGMAADK NKFPGDSVVT GRGRINGRLV YVFSQDFTVF GGSLSGAHAQ KICKIMDQAI TVGAPVIGLN D SGGARIQE ...String:
MAAALRVAAV GARLSVLASG LRAAVRSLCS QATSVNERIE NKRRTALLGG GQRRIDAQHK RGKLTARERI SLLLDPGSFV ESDMFVEHR CADFGMAADK NKFPGDSVVT GRGRINGRLV YVFSQDFTVF GGSLSGAHAQ KICKIMDQAI TVGAPVIGLN D SGGARIQE GVESLAGYAD IFLRNVTASG VIPQISLIMG PCAGGAVYSP ALTDFTFMVK DTSYLFITGP DVVKSVTNED VT QEELGGA KTHTTMSGVA HRAFENDVDA LCNLRDFFNY LPLSSQDPAP VRECHDPSDR LVPELDTIVP LESTKAYNMV DII HSVVDE REFFEIMPNY AKNIIVGFAR MNGRTVGIVG NQPKVASGCL DINSSVKGAR FVRFCDAFNI PLITFVDVPG FLPG TAQEY GGIIRHGAKL LYAFAEATVP KVTVITRKAY GGAYDVMSSK HLCGDTNYAW PTAEIAVMGA KGAVEIIFKG HENVE AAQA EYIEKFANPF PAAVRGFVDD IIQPSSTRAR ICCDLDVLAS KKVQRPWRKH ANIPL

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: 8
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: 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: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99377
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: COMMON LINE

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