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- PDB-3b96: Structural Basis for Substrate Fatty-Acyl Chain Specificity: Crys... -

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Basic information

Entry
Database: PDB / ID: 3b96
TitleStructural Basis for Substrate Fatty-Acyl Chain Specificity: Crystal Structure of Human Very-Long-Chain Acyl-CoA Dehydrogenase
ComponentsVery long-chain specific acyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / acyl-CoA / fatty acid beta-oxidation / dehydrogenase / very long chain / mitochondria / membrane / Acetylation / Alternative splicing / Cardiomyopathy / Disease mutation / FAD / Fatty acid metabolism / Flavoprotein / Lipid metabolism / Mitochondrion / Polymorphism / Transit peptide / Ubl conjugation
Function / homology
Function and homology information


energy derivation by oxidation of organic compounds / very-long-chain acyl-CoA dehydrogenase / very-long-chain fatty acyl-CoA dehydrogenase activity / Beta oxidation of palmitoyl-CoA to myristoyl-CoA / negative regulation of fatty acid oxidation / long-chain fatty acyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / fatty-acyl-CoA binding / negative regulation of fatty acid biosynthetic process ...energy derivation by oxidation of organic compounds / very-long-chain acyl-CoA dehydrogenase / very-long-chain fatty acyl-CoA dehydrogenase activity / Beta oxidation of palmitoyl-CoA to myristoyl-CoA / negative regulation of fatty acid oxidation / long-chain fatty acyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / fatty-acyl-CoA binding / negative regulation of fatty acid biosynthetic process / XBP1(S) activates chaperone genes / regulation of cholesterol metabolic process / temperature homeostasis / mitochondrial nucleoid / epithelial cell differentiation / response to cold / mitochondrial membrane / flavin adenine dinucleotide binding / mitochondrial inner membrane / mitochondrial matrix / nucleolus / mitochondrion / nucleoplasm / identical protein binding
Similarity search - Function
: / ACAD9/ACADV, C-terminal domain / 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 ...: / ACAD9/ACADV, C-terminal domain / 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
FLAVIN-ADENINE DINUCLEOTIDE / TETRADECANOYL-COA / Very long-chain specific acyl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.91 Å
AuthorsMcAndrew, R.P. / Wang, Y. / Mohsen, A.W. / He, M. / Vockley, J. / Kim, J.J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural basis for substrate fatty acyl chain specificity: crystal structure of human very-long-chain acyl-CoA dehydrogenase.
Authors: McAndrew, R.P. / Wang, Y. / Mohsen, A.W. / He, M. / Vockley, J. / Kim, J.J.
History
DepositionNov 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Very long-chain specific acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2233
Polymers63,4601
Non-polymers1,7632
Water7,945441
1
A: Very long-chain specific acyl-CoA dehydrogenase
hetero molecules

A: Very long-chain specific acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,4476
Polymers126,9202
Non-polymers3,5274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area15340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.616, 107.879, 149.776
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Very long-chain specific acyl-CoA dehydrogenase / VLCAD


Mass: 63459.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACADVL, VLCAD / Plasmid: pET-21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P49748, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors
#2: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 17.6% PEG 2000, 0.047 M MgCl2, 5% glycerol, pH 7.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
ROTATING ANODE11.5419
SYNCHROTRONAPS 19-ID21.0083
SYNCHROTRONAPS 5ID-B31.1405
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEMay 14, 2006
2CCDMay 14, 2006
3CCDMay 14, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Ni FilterSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
11.54191
21.00831
31.14051
ReflectionRedundancy: 5.4 % / Av σ(I) over netI: 7.8 / Number: 224137 / Rmerge(I) obs: 0.085 / Χ2: 1.6 / D res high: 1.95 Å / D res low: 50 Å / Num. obs: 41854 / % possible obs: 94.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.25099.910.0491.846.2
3.334.210010.0681.9456.4
2.913.3310010.0781.0786.2
2.652.9199.810.1261.2566
2.462.6599.810.170.9485.8
2.312.4699.310.2250.8755.6
2.22.319910.3231.9795.3
2.12.29710.4080.8844.6
2.022.185.710.5715.9483.5
1.952.0259.910.5280.7972.4
ReflectionResolution: 1.91→50 Å / Num. obs: 46776 / % possible obs: 98.8 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.079 / Χ2: 2.306 / Net I/σ(I): 15.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.91-1.986.70.53246301.53498.4
1.98-2.066.90.37345231.68897.4
2.06-2.1570.28945471.85697.2
2.15-2.267.10.21745912.06497.2
2.26-2.417.20.16946152.22598.7
2.41-2.597.50.13546862.24499.6
2.59-2.857.90.10147192.37399.9
2.85-3.278.40.07547522.563100
3.27-4.118.60.05147692.857100
4.11-508.30.04249443.199.7

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Phasing

PhasingMethod: MIRAS
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 46739
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.99-10025.90.871501
6.78-8.99190.928638
5.67-6.7826.30.906782
4.97-5.6721.20.914896
4.48-4.9718.50.9241018
4.11-4.4815.20.9381097
3.82-4.1115.70.921186
3.58-3.8214.40.9321269
3.39-3.5816.70.9231335
3.22-3.3919.70.9011410
3.07-3.2224.40.8831484
2.94-3.0756.60.8091529
2.83-2.9492.70.7361588
2.73-2.8390.60.7031652
2.64-2.73910.7331713
2.56-2.64890.7161781
2.48-2.5689.60.7391823
2.41-2.4892.30.6811858
2.35-2.4190.90.7051890
2.29-2.3590.50.7041974
2.24-2.2990.10.7351946
2.19-2.2488.10.6982016
2.14-2.1989.20.7332068
2.1-2.1491.10.7142075
2.05-2.191.40.7222150
2.01-2.0588.60.6792181
1.98-2.0190.40.6822211
1.94-1.9890.10.6382307
1.91-1.9491.40.6212361
Phasing MIR der
IDDer set-ID
11
21
Phasing MIR der site
IDDer-IDBiso (Å)Atom type symbolFract xFract yFract zOccupancy
1135.4654Hg0.88710.21790.11090.2056
1260Hg0.5010.0580.07560.0593
2160Os0.66270.17920.03250.3294

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.05phasing
DM4.2phasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MIRAS / Resolution: 1.91→30.69 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.004 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2371 5.1 %RANDOM
Rwork0.159 ---
obs0.162 46738 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.049 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.91→30.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4225 0 76 441 4742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224381
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9835912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0345552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.324.413179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29515760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.361523
X-RAY DIFFRACTIONr_chiral_restr0.1130.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023238
X-RAY DIFFRACTIONr_nbd_refined0.2210.22152
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23065
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2362
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.240
X-RAY DIFFRACTIONr_mcbond_it3.7281.52822
X-RAY DIFFRACTIONr_mcangle_it4.22124371
X-RAY DIFFRACTIONr_scbond_it7.01931806
X-RAY DIFFRACTIONr_scangle_it9.7174.51541
LS refinement shellResolution: 1.91→1.957 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 165 -
Rwork0.234 3122 -
all-3287 -
obs--95.83 %

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