+Open data
-Basic information
Entry | Database: PDB / ID: 8rth | ||||||
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Title | Trypanosoma brucei 3-methylcrotonyl-CoA carboxylase | ||||||
Components |
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Keywords | TRANSFERASE / carboxylase / trypanosoma brucei / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Function and homology information methylcrotonoyl-CoA carboxylase / methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / L-leucine catabolic process / pyrimidine nucleobase biosynthetic process / biotin binding / cilium / mitochondrion / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.37 Å | ||||||
Authors | Ruiz, F.M. / Plaza-Pegueroles, A. / Fernandez-Tornero, C. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Structure / Year: 2024 Title: The cryo-EM structure of trypanosome 3-methylcrotonyl-CoA carboxylase provides mechanistic and dynamic insights into its enzymatic function. Authors: Adrián Plaza-Pegueroles / Inna Aphasizheva / Ruslan Aphasizhev / Carlos Fernández-Tornero / Federico M Ruiz / Abstract: 3-Methylcrotonyl-CoA carboxylase (MCC) catalyzes the two-step, biotin-dependent production of 3-methylglutaconyl-CoA, an essential intermediate in leucine catabolism. Given the critical metabolic ...3-Methylcrotonyl-CoA carboxylase (MCC) catalyzes the two-step, biotin-dependent production of 3-methylglutaconyl-CoA, an essential intermediate in leucine catabolism. Given the critical metabolic role of MCC, deficiencies in this enzyme lead to organic aciduria, while its overexpression is linked to tumor development. MCC is a dodecameric enzyme composed of six copies of each α- and β-subunit. We present the cryo-EM structure of the endogenous MCC holoenzyme from Trypanosoma brucei in a non-filamentous state at 2.4 Å resolution. Biotin is covalently bound to the biotin carboxyl carrier protein domain of α-subunits and positioned in a non-canonical pocket near the active site of neighboring β-subunit dimers. Moreover, flexibility of key residues at α-subunit interfaces and loops enables pivoting of α-subunit trimers to partly reduce the distance between α- and β-subunit active sites, required for MCC catalysis. Our results provide a structural framework to understand the enzymatic mechanism of eukaryotic MCCs and to assist drug discovery against trypanosome infections. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rth.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8rth.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 8rth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rth_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8rth_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8rth_validation.xml.gz | 186.1 KB | Display | |
Data in CIF | 8rth_validation.cif.gz | 284.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/8rth ftp://data.pdbj.org/pub/pdb/validation_reports/rt/8rth | HTTPS FTP |
-Related structure data
Related structure data | 19492MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 73987.648 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57YQ4 #2: Protein | Mass: 66613.969 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) References: UniProt: Q385A6, methylcrotonoyl-CoA carboxylase #3: Chemical | ChemComp-BTI / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 3-methylcrotonyl-CoA carboxylase / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Trypanosoma brucei (eukaryote) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.07 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 38.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 490000 | ||||||||||||||||||||||||
Symmetry | Point symmetry: D3 (2x3 fold dihedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126391 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Atomic model building |
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