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- PDB-1v11: CROSSTALK BETWEEN COFACTOR BINDING AND THE PHOSPHORYLATION LOOP C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1v11 | |||||||||
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Title | CROSSTALK BETWEEN COFACTOR BINDING AND THE PHOSPHORYLATION LOOP CONFORMATION IN THE BCKD MACHINE | |||||||||
![]() | (2-OXOISOVALERATE DEHYDROGENASE ...) x 2 | |||||||||
![]() | OXIDOREDUCTASE / KETOACID DEHYDROGENASE / BRANCHED-CHAIN / MULTI-ENZYME COMPLEX / ACYLATION / OXIDATIVE DECARBOXYLATION / MAPLE SYRUP URINE DISEASE / THIAMINE PHOSPHATE / PHOSPHORYLATION | |||||||||
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 / carboxy-lyase activity / Glyoxylate metabolism and glycine degradation / response to glucocorticoid / response to cAMP ...: / 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 / carboxy-lyase activity / Glyoxylate metabolism and glycine degradation / 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Li, J. / Wynn, R.M. / Machius, M. / Chuang, J.L. / Karthikeyan, S. / Tomchick, D.R. / Chuang, D.T. | |||||||||
![]() | ![]() Title: Cross-Talk between Thiamin Diphosphate Binding and Phosphorylation Loop Conformation in Human Branched-Chain {Alpha}-Keto Acid Decarboxylase/Dehydrogenase Authors: Li, J. / Wynn, R.M. / Machius, M. / Chuang, J.L. / Karthikeyan, S. / Tomchick, D.R. / Chuang, D.T. #1: ![]() 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. #2: Journal: J.Biol.Chem. / Year: 2003 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. #3: ![]() 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 | ![]() | 172.8 KB | Display | ![]() |
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PDB format | ![]() | 133.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 795.8 KB | Display | ![]() |
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Full document | ![]() | 804.4 KB | Display | |
Data in XML | ![]() | 32.7 KB | Display | |
Data in CIF | ![]() | 49 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1v16C ![]() 1v1mC ![]() 1v1rC ![]() 1olsS 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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Unit cell |
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Components on special symmetry positions |
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Components
-2-OXOISOVALERATE DEHYDROGENASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 45417.914 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: EXPRESSION SYSTEM USED BL-21 CELLS WITH OVEREXPRESSING GROEL AND GROES Plasmid: PTRC-ALPHA-BETAHIS / Production host: ![]() ![]() 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: EXPRESSION SYSTEM USED BL-21 CELLS WITH OVEREXPRESSING GROEL AND GROES Plasmid: PTRC-ALPHA-BETAHIS / Production host: ![]() ![]() References: UniProt: P21953, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) |
-Non-polymers , 7 types, 542 molecules ![](data/chem/img/K.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TPP.gif)
![](data/chem/img/BEN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TPP.gif)
![](data/chem/img/BEN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-MN / | #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-TPP / | #7: Chemical | ChemComp-BEN / | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED MUTATION IN CHAIN A, ARG 332 TO ALA FUNCTION: THE BRANCHED-CHAIN ALPHA-KETO ...ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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 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: Jul 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: 1.95→33.35 Å / Num. obs: 61649 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 6 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OLS Resolution: 1.95→27.52 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.456 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.75 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→27.52 Å
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Refine LS restraints |
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