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Yorodumi- PDB-1v1r: CROSSTALK BETWEEN COFACTOR BINDING AND THE PHOSPHORYLATION LOOP C... -
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-Basic information
Entry | Database: PDB / ID: 1v1r | ||||||
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Title | CROSSTALK BETWEEN COFACTOR BINDING AND THE PHOSPHORYLATION LOOP CONFORMATION IN THE BCKD MACHINE | ||||||
Components | (2-OXOISOVALERATE DEHYDROGENASE ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / KETOACID DEHYDROGENASE / MULTI-ENZYME COMPLEX / ACYLATION / OXIDATIVE DECARBOXYLATION / MAPLE SYRUP URINE DISEASE / THIAMIN DIPHOSPHATE / PHOSPHORYLATION / FLAVOPROTEIN | ||||||
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 / 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Li, J. / Wynn, R.M. / Machius, M. / Chuang, J.L. / Karthikeyan, S. / Tomchick, D.R. / Chuang, D.T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 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: 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. #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: Journal: Structure / Year: 2000 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v1r.cif.gz | 168.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v1r.ent.gz | 131.8 KB | Display | PDB format |
PDBx/mmJSON format | 1v1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v1r_validation.pdf.gz | 464.7 KB | Display | wwPDB validaton report |
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Full document | 1v1r_full_validation.pdf.gz | 472.4 KB | Display | |
Data in XML | 1v1r_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 1v1r_validation.cif.gz | 48.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/1v1r ftp://data.pdbj.org/pub/pdb/validation_reports/v1/1v1r | HTTPS FTP |
-Related structure data
Related structure data | 1v11C 1v16C 1v1mC 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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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: 45504.031 Da / Num. of mol.: 1 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): 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 Source method: isolated from a genetically manipulated source Details: APO-FORM / Source: (gene. exp.) HOMO SAPIENS (human) Description: EXPRESSION SYSTEM USED BL-21 CELLS WITH OVEREXPRESSING GROEL AND GROES Plasmid: PTRC-ALPHA-BETAHIS / Production host: ESCHERICHIA COLI (E. coli) Strain (production host): BL-21 CELLS WITH OVEREXPRESSING GROEL AND GROES References: UniProt: P21953, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) |
-Non-polymers , 6 types, 541 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Compound details | FUNCTION: THE BRANCHED-CHAIN ALPHA-KETO DEHYDROGENASE COMPLEX CATALYZES THE OVERALL CONVERSION OF ...FUNCTION: THE BRANCHED-CHAIN ALPHA-KETO DEHYDROGEN |
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-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 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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97967 |
Detector | Detector: CCD / Date: Jun 6, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97967 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→32.14 Å / Num. obs: 77214 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.835 / Mean I/σ(I) obs: 2 / % possible all: 97.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OLS Resolution: 1.8→23.77 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.248 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.095 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→23.77 Å
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Refine LS restraints |
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