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- PDB-1olx: Roles of His291-alpha and His146-beta' in the reductive acylation... -
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Basic information
Entry | Database: PDB / ID: 1olx | |||||||||
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Title | Roles of His291-alpha and His146-beta' in the reductive acylation reaction catalyzed by human branched-chain alpha-ketoacid dehydrogenase | |||||||||
![]() | (2-OXOISOVALERATE DEHYDROGENASE ...) x 2 | |||||||||
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Function / homology | ![]() : / 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 / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wynn, R.M. / Machius, M. / Chuang, J.L. / Li, J. / Tomchick, D.R. / Chuang, D.T. | |||||||||
![]() | ![]() 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.M. / Machius, M. / Chuang, J.L. / Li, J. / Tomchick, D.R. / Chuang, D.T. #1: Journal: J.Biol.Chem. / Year: 2001 Title: Roles of Active Site and Novel K+ 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. #2: ![]() Title: Crystal Structure of Human Branched-Chain Alpha-Ketoacid Dehydrogenase and the Molecular Basis of Multienzyme Complex Deficiency in Maple Syrup Urine Disease Authors: Aevarsson, A. / Chuang, J.L. / Wynn, R.M. / Turley, S. / Chuang, D.T. / Hol, W.G.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.8 KB | Display | ![]() |
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PDB format | ![]() | 130.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1olsSC ![]() 1oluC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-2-OXOISOVALERATE DEHYDROGENASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 45571.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P12694, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) |
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#2: Protein | Mass: 37835.203 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P21953, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) |
-Non-polymers , 5 types, 377 molecules ![](data/chem/img/K.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/TPP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/TPP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-MN / | #5: Chemical | ChemComp-TPP / | ![]() #6: Chemical | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Details
Compound details | THE BRANCHED-CHAIN ALPHA-KETO DEHYDROGENASE COMPLEX CATALYZES CONVERSION OF ALPHA-KETO ACIDS TO ...THE BRANCHED-CHAIN ALPHA-KETO DEHYDROGEN |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % |
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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 MN2+ IONS COULD REPLACE THE MG2+ REQUIRED FOR THE BINDING OF THDP TO THE ENZYME. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Mar 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.25→32.18 Å / Num. obs: 37471 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.25→2.25 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 1.6 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1OLS Resolution: 2.25→32.18 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 372026.51 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE FOLLOWING REGION HAD VERY POOR ELECTRON DENSITY: ALPHA CHAIN: RESIDUES 183-184, 294, 296, 298-300,307-312 BETA CHAIN: RESIDUES 5, 14, 17, 235. SIDE CHAINS OF THE FOLLOWING RESIDUES DID ...Details: THE FOLLOWING REGION HAD VERY POOR ELECTRON DENSITY: ALPHA CHAIN: RESIDUES 183-184, 294, 296, 298-300,307-312 BETA CHAIN: RESIDUES 5, 14, 17, 235. SIDE CHAINS OF THE FOLLOWING RESIDUES DID HAVE POORLY DEFINED ELECTRON DENSITY AND WERE MODELLED STEREOCHEMICALLY: ALPHA CHAIN: K19, A183, E331, K335, R338, K339, Q387 BETA CHAIN: Q7
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.6078 Å2 / ksol: 0.378655 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→32.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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