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Yorodumi- PDB-2beu: Reactivity modulation of human branched-chain alpha-ketoacid dehy... -
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- Basic information
Basic information
| Entry | Database: PDB / ID: 2beu | ||||||
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| Title | Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch | ||||||
|  Components | 
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|  Keywords | OXIDOREDUCTASE / OXIDATIVE DECARBOXYLATION / MAPLE SYRUP URINE DISEASE / THIAMINE DIPHOSPHATE / PHOSPHORYLATION / CONFORMATIONAL SWITCH | ||||||
| Function / homology |  Function and homology information Loss-of-function mutations in BCKDHA or BCKDHB cause MSUD / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / branched-chain 2-oxo acid dehydrogenase activity / branched-chain alpha-ketoacid dehydrogenase complex / BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV / Loss-of-function mutations in DBT cause MSUD2 / Loss-of-function mutations in DLD cause MSUD3/DLDD / H139Hfs13* PPM1K causes a mild variant of  MSUD / Branched-chain ketoacid dehydrogenase kinase deficiency / branched-chain amino acid catabolic process ...Loss-of-function mutations in BCKDHA or BCKDHB cause MSUD / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / branched-chain 2-oxo acid dehydrogenase activity / branched-chain alpha-ketoacid dehydrogenase complex / BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV / Loss-of-function mutations in DBT cause MSUD2 / Loss-of-function mutations in DLD cause MSUD3/DLDD / H139Hfs13* PPM1K causes a mild variant of  MSUD / Branched-chain ketoacid dehydrogenase kinase deficiency / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / carboxy-lyase activity / response to nutrient / lipid metabolic process / mitochondrial matrix / nucleolus / mitochondrion / nucleoplasm / metal ion binding Similarity search - Function | ||||||
| Biological species |  HOMO SAPIENS (human) SYNTHETIC CONSTRUCT (others) | ||||||
| Method |  X-RAY DIFFRACTION /  SYNCHROTRON /  FOURIER SYNTHESIS / Resolution: 1.89 Å | ||||||
|  Authors | Machius, M. / Wynn, R.M. / Chuang, J.L. / Tomchick, D.R. / Brautigam, C.A. / Chuang, D.T. | ||||||
|  Citation |  Journal: Structure / Year: 2006 Title: A Versatile Conformational Switch Regulates Reactivity in Human Branched-Chain Alpha-Ketoacid Dehydrogenase. Authors: Machius, M. / Wynn, R.M. / Chuang, J.L. / Li, J. / Kluger, R. / Yu, D. / Tomchick, D.R. / Brautigam, C.A. / Chuang, D.T. #1:   Journal: J.Biol.Chem. / Year: 2004 Title: Crosstalk between Cofactor Binding and the Phosphorylation Loop Conformation in the Bckd Machine Authors: Li, J. / Wynn, R.M. / Machius, M. / Chuang, J.L. / Karthikeyan, S. / Tomchick, D.R. / Chuang, D.T. #2:   Journal: J.Biol.Chem. / Year: 2003 Title: Roles of His291-Alpha and His146-Beta in the Reductive Acylation Reaction Catalyzed by Human Branched-Chain Alpha-Ketoacid Dehydrogenase: Refined Phosphorylation Loop Structure in the Active Site Authors: Wynn, R. / Machius, M. / Chuang, J. / Li, J. / Tomchick, D. / Chuang, D. #3: Journal: J.Biol.Chem. / Year: 2001 Title: Roles of Active Site and Novel Potassium Ion- Binding Site Residues in Human Mitochondrial Branched-Chain Alpha-Ketoacid Decarboxylase- Dehydrogenase Authors: Wynn, R.M. / Ho, R. / Chuang, J.L. / Chuang, D.T. | ||||||
| History | 
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- Structure visualization
Structure visualization
| Structure viewer | Molecule:  Molmil  Jmol/JSmol | 
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- Downloads & links
Downloads & links
- Download
Download
| PDBx/mmCIF format |  2beu.cif.gz | 175.9 KB | Display |  PDBx/mmCIF format | 
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| PDB format |  pdb2beu.ent.gz | 135.7 KB | Display |  PDB format | 
| PDBx/mmJSON format |  2beu.json.gz | Tree view |  PDBx/mmJSON format | |
| Others |  Other downloads | 
-Validation report
| Summary document |  2beu_validation.pdf.gz | 810.7 KB | Display |  wwPDB validaton report | 
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| Full document |  2beu_full_validation.pdf.gz | 822.3 KB | Display | |
| Data in XML |  2beu_validation.xml.gz | 33.8 KB | Display | |
| Data in CIF |  2beu_validation.cif.gz | 50 KB | Display | |
| Arichive directory |  https://data.pdbj.org/pub/pdb/validation_reports/be/2beu  ftp://data.pdbj.org/pub/pdb/validation_reports/be/2beu | HTTPS FTP | 
-Related structure data
| Related structure data |  1wciC  2bevC  2bewC  2bfbC  2bfcC  2bfdC  2bfeC  2bffC  1olsS S: Starting model for refinement C: citing same article ( | 
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| Similar structure data | 
- Links
Links
- Assembly
Assembly
| Deposited unit |  
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| 1 |  
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| Unit cell | 
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| Components on special symmetry positions | 
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| Details | THIS PROTEIN IS A ALPHA-BETA TETRAMER, BUT INTHE PRESENT ENTRY, THEY ARE IN COMPLEX WITH A PEPTIDECHAIN C, THEREBY MAKING THE WHOLE ASSEMBLY A HEXAMERCHAIN C IS A FRAGMENT OF CHAIN B. IT IS NOT CLEAR WHETHERTHIS FRAGMENT IS AN ALTERNATIVE CONFORMATION OF THE CORRESPONDINGRESIDUES IN CHAIN B OF THE SAME MOLECULE OR OF A NEIGHBORING,SYMMETRY-RELATED MOLECULE. IT COULD ALSO COME FROM PROTEOLYSIS,BUT THE AUTHORS DO NOT HAVE ANY EVIDENCE FOR THAT. | 
- Components
Components
-2-OXOISOVALERATE DEHYDROGENASE  ... , 2 types, 2 molecules AB 
| #1: Protein | Mass: 45571.098 Da / Num. of mol.: 1 / Fragment: RESIDUES 46-445 Source method: isolated from a genetically manipulated source Source: (gene. exp.)  HOMO SAPIENS (human) / Plasmid: PTRC-ALPHA-BETAHIS / Production host:   ESCHERICHIA COLI BL21 (bacteria) Variant (production host): BL-21 CELLS WITH OVEREXPRESSING GROEL AND GROES References: UniProt: P12694, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) | 
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| #2: Protein | Mass: 37902.270 Da / Num. of mol.: 1 / Fragment: RESIDUES 51-392 Source method: isolated from a genetically manipulated source Source: (gene. exp.)  HOMO SAPIENS (human) / Plasmid: PTRC-ALPHA-BETAHIS / Production host:   ESCHERICHIA COLI BL21 (bacteria) Variant (production host): BL-21 CELLS WITH OVEREXPRESSING GROEL AND GROES References: UniProt: P21953, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) | 
-Protein/peptide , 1 types, 1 molecules C
| #3: Protein/peptide | Mass: 409.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) | 
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-Non-polymers , 7 types, 513 molecules 












| #4: Chemical | | #5: Chemical | ChemComp-THV / | #6: Chemical | #7: Chemical | ChemComp-MN / | #8: Chemical | ChemComp-SO4 / | #9: Chemical | ChemComp-GOL / | #10: Water | ChemComp-HOH / |  | 
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-Details
| Sequence details | CHAIN C IS A FRAGMENT OF CHAIN B. IT IS NOT CLEAR WHETHER THIS FRAGMENT IS AN ALTERNATIVE  ...CHAIN C IS A FRAGMENT OF CHAIN B. IT IS NOT CLEAR WHETHER THIS FRAGMENT IS AN ALTERNATIV | 
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-Experimental details
-Experiment
| Experiment | Method:  X-RAY DIFFRACTION / Number of used crystals: 1 | 
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- Sample preparation
Sample preparation
| Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 53.4 % | 
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| Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: CRYSTALS WERE GROWN AT 20C VIA THE VAPOR DIFFUSION METHOD BY MIXING EQUAL AMOUNTS OF PROTEIN (20-25 MG/ML IN 50 MM HEPES/NAOH, PH 7.5, 250 MM KCL, 0.5 MM PMSF, 1 MM BENZAMIDINE AND 5% (V/V) ...Details: CRYSTALS WERE GROWN AT 20C VIA THE VAPOR DIFFUSION METHOD BY MIXING EQUAL AMOUNTS OF PROTEIN (20-25 MG/ML IN 50 MM HEPES/NAOH, PH 7.5, 250 MM KCL, 0.5 MM PMSF, 1 MM BENZAMIDINE AND 5% (V/V) GLYCEROL) WITH WELL SOLUTION (1.4- 1.6 M AMMONIUM SULFATE, 0.1 M NA-CITRATE PH 5.8, 20 MM B-MERCAPTOETHANOL). SERIALLY DILUTED CRUSHED CRYSTALS WERE USED FOR MICRO-SEEDING ONE DAY AFTER THE DROPS WERE SET UP. CRYSTALS APPEARED ONE DAY AFTER SEEDING AND GREW TO A MAXIMUM SIZE OF 120 X 800 UM WITHIN 10 DAYS. CRYSTALS WERE STABILIZED FOR 12 HOURS BY TRANSFER TO FRESH WELL SOLUTION. THEY WERE THEN CRYO-PROTECTED BY STEP-WISE TRANSFER INTO CRYO-BUFFER CONTAINING 1.6 M AMMONIUM SULFATE, 50 MM HEPES, PH 7.5, 100 MM NA-CITRATE, PH 5.8, 100 MM KCL, 50 MM DTT AND UP TO 20% (V/V) GLYCEROL. IT WAS FOUND THAT MANGANESE IONS COULD REPLACE THE MAGNESIUM REQUIRED FOR THE BINDING OF THDP TO THE ENZYME. | 
-Data collection
| Diffraction | Mean temperature: 100 K | 
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| Diffraction source | Source:  SYNCHROTRON / Site:  APS  / Beamline: 19-BM / Wavelength: 1.00691 | 
| Detector | Type: CUSTOM / Detector: CCD / Date: Jun 21, 2003 | 
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | 
| Radiation wavelength | Wavelength: 1.00691 Å / Relative weight: 1 | 
| Reflection | Resolution: 1.88→25.61 Å / Num. obs: 65878 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 22.65 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.3 | 
| Reflection shell | Resolution: 1.88→1.91 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8 | 
- Processing
Processing
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| Refinement | Method to determine structure:  FOURIER SYNTHESIS Starting model: PDB ENTRY 1OLS Resolution: 1.89→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.578 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY 
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso  mean: 17.14 Å2 
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| Refinement step | Cycle: LAST / Resolution: 1.89→30 Å 
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| Refine LS restraints | 
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