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Yorodumi- PDB-2bev: Reactivity modulation of human branched-chain alpha-ketoacid dehy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bev | ||||||
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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 : / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / Glyoxylate metabolism and glycine degradation / carboxy-lyase activity / response to glucocorticoid / response to cAMP / response to nutrient ...: / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / Glyoxylate metabolism and glycine degradation / carboxy-lyase activity / response to glucocorticoid / response to cAMP / response to nutrient / lipid metabolic process / mitochondrial matrix / protein-containing complex binding / 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: 1.8 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 viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bev.cif.gz | 182.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bev.ent.gz | 142 KB | Display | PDB format |
PDBx/mmJSON format | 2bev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/2bev ftp://data.pdbj.org/pub/pdb/validation_reports/be/2bev | HTTPS FTP |
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-Related structure data
Related structure data | 1wciC 2beuC 2bewC 2bfbC 2bfcC 2bfdC 2bfeC 2bffC 1olsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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
-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 (E. coli) / Strain (production host): BL21 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 (E. coli) / Strain (production host): BL21 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 , 6 types, 701 molecules
#4: Chemical | ChemComp-THY / | ||||||||
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#5: Chemical | #6: Chemical | ChemComp-MN / | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
-Details
Compound details | CATALYTIC ACTIVITY: 3-METHYL-2-OXOBUTANOATE + [DIHYDROLIPOYLLYSINE-RESIDUE (2-METHYLPROPANOYL) ...CATALYTIC ACTIVITY: 3-METHYL-2-OXOBUTANOA |
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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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-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-ID / Wavelength: 1.00691 |
Detector | Type: CUSTOM / Detector: CCD / Date: Jun 25, 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: 1.8→32.05 Å / Num. obs: 77268 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1OLS Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.616 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.091 / 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: 13.26 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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