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- PDB-2r0m: The effect of a Glu370Asp Mutation in Glutaryl-CoA Dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 2r0m
TitleThe effect of a Glu370Asp Mutation in Glutaryl-CoA Dehydrogenase on Proton Transfer to the Dienolate Intermediate
ComponentsGlutaryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Glutaryl-CoA Dehydrogenase / Flavoprotein / isomerase / Alternative splicing / Disease mutation / FAD / Mitochondrion / Polymorphism / Transit peptide
Function / homology
Function and homology information


glutaryl-CoA dehydrogenase (ETF) / glutaryl-CoA dehydrogenase activity / fatty-acyl-CoA biosynthetic process / tryptophan metabolic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase / Lysine catabolism / fatty-acyl-CoA binding / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion
Similarity search - Function
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 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
4-nitrobutanoic acid / FLAVIN-ADENINE DINUCLEOTIDE / Glutaryl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRao, K.S. / Fu, Z. / Albro, M. / Narayanan, B. / Baddam, S. / Lee, H.J. / Kim, J.J. / Frerman, F.E.
CitationJournal: Biochemistry / Year: 2007
Title: The effect of a Glu370Asp mutation in glutaryl-CoA dehydrogenase on proton transfer to the dienolate intermediate.
Authors: Rao, K.S. / Fu, Z. / Albro, M. / Narayanan, B. / Baddam, S. / Lee, H.J. / Kim, J.J. / Frerman, F.E.
History
DepositionAug 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4213
Polymers43,5031
Non-polymers9192
Water86548
1
A: Glutaryl-CoA dehydrogenase
hetero molecules

A: Glutaryl-CoA dehydrogenase
hetero molecules

A: Glutaryl-CoA dehydrogenase
hetero molecules

A: Glutaryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,68512
Polymers174,0114
Non-polymers3,6758
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.880, 116.880, 128.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Glutaryl-CoA dehydrogenase / / GCD


Mass: 43502.676 Da / Num. of mol.: 1 / Mutation: E370D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q92947, glutaryl-CoA dehydrogenase
#2: 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
#3: Chemical ChemComp-4NI / 4-nitrobutanoic acid


Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES buffer pH 6.5, 30% PEGMME5000, 200 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 15, 2003 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→28.07 Å / Num. all: 32297 / Num. obs: 12017 / % possible obs: 81.4 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 19.6 Å2 / Rsym value: 0.153 / Net I/σ(I): 7.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1076 / Rsym value: 0.337 / % possible all: 75.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SIQ

1siq


Resolution: 2.7→28.07 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 251131.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1240 10.3 %RANDOM
Rwork0.191 ---
obs-12000 81.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.3641 Å2 / ksol: 0.32995 e/Å3
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.07 Å21.89 Å20 Å2
2--3.07 Å20 Å2
3----6.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.7→28.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 62 48 3120
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.312.5
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.345 119 11 %
Rwork0.312 962 -
obs--75.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4fad.parfad.top
X-RAY DIFFRACTION54nb.par4nb.top

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