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- PDB-1egd: STRUCTURE OF T255E, E376G MUTANT OF HUMAN MEDIUM CHAIN ACYL-COA D... -

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Basic information

Entry
Database: PDB / ID: 1egd
TitleSTRUCTURE OF T255E, E376G MUTANT OF HUMAN MEDIUM CHAIN ACYL-COA DEHYDROGENASE
ComponentsMEDIUM CHAIN ACYL-COA DEHYDROGENASE
KeywordsELECTRON TRANSFER / ACYL-COA DEHYDROGENASE / FLAVOPROTEIN
Function / homology
Function and homology information


medium-chain fatty acid catabolic process / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / carnitine metabolic process, CoA-linked / medium-chain acyl-CoA dehydrogenase / medium-chain fatty acyl-CoA dehydrogenase activity / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / carnitine biosynthetic process / medium-chain fatty acid metabolic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase ...medium-chain fatty acid catabolic process / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / carnitine metabolic process, CoA-linked / medium-chain acyl-CoA dehydrogenase / medium-chain fatty acyl-CoA dehydrogenase activity / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / carnitine biosynthetic process / medium-chain fatty acid metabolic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / cardiac muscle cell differentiation / glycogen biosynthetic process / regulation of gluconeogenesis / response to starvation / fatty acid beta-oxidation / response to cold / post-embryonic development / liver development / PPARA activates gene expression / mitochondrial membrane / flavin adenine dinucleotide binding / mitochondrial matrix / axon / mitochondrion / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Medium-chain specific acyl-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 / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal ...Medium-chain specific acyl-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 / 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, N-terminal domain / Acyl-CoA dehydrogenase, C-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 oxidase/dehydrogenase, middle domain superfamily / 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 / Medium-chain specific acyl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsLee, H.J. / Wang, M. / Paschke, R. / Nandy, A. / Ghisla, S. / Kim, J.P.
CitationJournal: Biochemistry / Year: 1996
Title: Crystal structures of the wild type and the Glu376Gly/Thr255Glu mutant of human medium-chain acyl-CoA dehydrogenase: influence of the location of the catalytic base on substrate specificity.
Authors: Lee, H.J. / Wang, M. / Paschke, R. / Nandy, A. / Ghisla, S. / Kim, J.J.
History
DepositionApr 11, 1996Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MEDIUM CHAIN ACYL-COA DEHYDROGENASE
B: MEDIUM CHAIN ACYL-COA DEHYDROGENASE
C: MEDIUM CHAIN ACYL-COA DEHYDROGENASE
D: MEDIUM CHAIN ACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,7498
Polymers174,6074
Non-polymers3,1424
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23560 Å2
ΔGint-169 kcal/mol
Surface area50960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.180, 170.180, 150.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
MEDIUM CHAIN ACYL-COA DEHYDROGENASE


Mass: 43651.762 Da / Num. of mol.: 4 / Mutation: T255E, E376G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P11310, EC: 1.3.99.3
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 49 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
2140 mMTris acetate1drop
38.0 %(w/v)PEG40001drop
450 %PEG40001reservoir
1enzyme1drop0.027mg

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 18, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 66928 / % possible obs: 77.7 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.072
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. measured all: 204212 / Rmerge(I) obs: 0.0729

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
R-AXISIICdata reduction
X-PLORphasing
RefinementResolution: 2.4→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.208 -
obs0.208 66928
Displacement parametersBiso mean: 21.96 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11960 0 212 230 12402
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.969 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg22.5
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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