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- PDB-1ivh: STRUCTURE OF HUMAN ISOVALERYL-COA DEHYDROGENASE AT 2.6 ANGSTROMS ... -

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Basic information

Entry
Database: PDB / ID: 1ivh
TitleSTRUCTURE OF HUMAN ISOVALERYL-COA DEHYDROGENASE AT 2.6 ANGSTROMS RESOLUTION: STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY
ComponentsISOVALERYL-COA DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ACYL-COA DEHYDROGENASE / FLAVOPROTEIN / ISOVALERYL-COA / ISOVALERIC ACIDEMIA
Function / homology
Function and homology information


isovaleryl-CoA dehydrogenase / isovaleryl-CoA dehydrogenase activity / short-chain acyl-CoA dehydrogenase / butyryl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / L-leucine catabolic process / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / flavin adenine dinucleotide binding / mitochondrial matrix ...isovaleryl-CoA dehydrogenase / isovaleryl-CoA dehydrogenase activity / short-chain acyl-CoA dehydrogenase / butyryl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / L-leucine catabolic process / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding
Similarity search - Function
Isovaleryl-CoA dehydrogenase / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal ...Isovaleryl-CoA dehydrogenase / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COENZYME A PERSULFIDE / FLAVIN-ADENINE DINUCLEOTIDE / Isovaleryl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTiffany, K.A. / Roberts, D.L. / Wang, M. / Paschke, R. / Mohsen, A.-W.A. / Vockley, J. / Kim, J.J.P.
CitationJournal: Biochemistry / Year: 1997
Title: Structure of human isovaleryl-CoA dehydrogenase at 2.6 A resolution: structural basis for substrate specificity,.
Authors: Tiffany, K.A. / Roberts, D.L. / Wang, M. / Paschke, R. / Mohsen, A.W. / Vockley, J. / Kim, J.J.
History
DepositionMay 15, 1997Processing site: BNL
Revision 1.0May 20, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ISOVALERYL-COA DEHYDROGENASE
B: ISOVALERYL-COA DEHYDROGENASE
C: ISOVALERYL-COA DEHYDROGENASE
D: ISOVALERYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,82312
Polymers172,4824
Non-polymers6,3418
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26500 Å2
ΔGint-138 kcal/mol
Surface area46950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.000, 97.700, 181.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ISOVALERYL-COA DEHYDROGENASE /


Mass: 43120.477 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: EACH SUBUNIT CONTAINS ONE NON-COVALENTLY BOUND FAD MOLECULE AND ONE NON-COVALENTLY BOUND COA PER SULFIDE MOLECULE
Source: (gene. exp.) Homo sapiens (human)
Description: THE CDNA WAS ALTERED TO ACCOMMODATE ESCHERICHIA COLI CODON USAGE IN ORDER TO ACHIEVE A HIGH LEVEL OF EXPRESSION. THE MOLECULE WAS THEN CLONED, EXPRESSED, AND PURIFIED AS DESCRIBED IN\: ...Description: THE CDNA WAS ALTERED TO ACCOMMODATE ESCHERICHIA COLI CODON USAGE IN ORDER TO ACHIEVE A HIGH LEVEL OF EXPRESSION. THE MOLECULE WAS THEN CLONED, EXPRESSED, AND PURIFIED AS DESCRIBED IN\: MOHSEN, A.W. AND VOCKLEY, J. (1995) BIOCHEMISTRY, 34\:10146-10152
Gene: IVD / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / Plasmid: PKMHIVD / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P26440, isovaleryl-CoA dehydrogenase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-COS / COENZYME A PERSULFIDE


Mass: 799.599 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOA PERSULFIDE WAS MODELED INTO THE ACTIVE SITE AS DESCRIBED BY TIFFANY ET AL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 51 % / Description: A HOMOTETRAMER WAS USED AS THE SEARCH MODEL
Crystal growTemperature: 292 K / pH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 8% PEG 8000, 0.1 M TRIS, PH 8.5 AT 19 DEGREES CELSIUS., temperature 292K
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlhuman IVD1drop
24 %(w/v)PEG80001drop
350 mMTris-HCl1drop
48 %(w/v)PEG80001reservoir
5100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 42529 / % possible obs: 82.2 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 11.5
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.219 / % possible all: 61
Reflection shell
*PLUS
% possible obs: 61 % / Rmerge(I) obs: 0.219

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MDE

1mde


Resolution: 2.6→10 Å / Rfactor Rfree error: 0.002 / Cross valid method: FREE R / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2702 10 %RANDOM
Rwork0.207 ---
obs0.207 37968 82.5 %-
Displacement parametersBiso mean: 12 Å2
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11844 0 408 215 12467
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.53
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.327 230 8.3 %
Rwork0.283 2760 -
obs--50.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDXJ.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARS.COATOP.COA
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.53
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3
LS refinement shell
*PLUS
Rfactor obs: 0.283

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