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- PDB-1ey3: STRUCTURE OF ENOYL-COA HYDRATASE COMPLEXED WITH THE SUBSTRATE DAC-COA -

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Basic information

Entry
Database: PDB / ID: 1ey3
TitleSTRUCTURE OF ENOYL-COA HYDRATASE COMPLEXED WITH THE SUBSTRATE DAC-COA
ComponentsENOYL-COA HYDRATASE
KeywordsLYASE / BETA-OXIDATION / CROTONASE / ENOYL-COA HYDRATASE / FATTY ACID METABOLISM / BETA-ELIMINATION / SYN-ADDITION / CONCERTED REACTION
Function / homology
Function and homology information


Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / 3-hydroxypropionyl-CoA dehydratase activity / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / crotonyl-CoA hydratase activity / Branched-chain amino acid catabolism / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity ...Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / 3-hydroxypropionyl-CoA dehydratase activity / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / crotonyl-CoA hydratase activity / Branched-chain amino acid catabolism / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / enoyl-CoA hydratase / enoyl-CoA hydratase activity / fatty acid beta-oxidation / mitochondrial matrix / mitochondrion
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-(N,N-DIMETHYLAMINO)CINNAMOYL-COA / Enoyl-CoA hydratase, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsBahnson, B.J. / Anderson, V.E. / Petsko, G.A.
CitationJournal: Biochemistry / Year: 2002
Title: Structural mechanism of enoyl-CoA hydratase: three atoms from a single water are added in either an E1cb stepwise or concerted fashion.
Authors: Bahnson, B.J. / Anderson, V.E. / Petsko, G.A.
History
DepositionMay 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: 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
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENOYL-COA HYDRATASE
B: ENOYL-COA HYDRATASE
C: ENOYL-COA HYDRATASE
D: ENOYL-COA HYDRATASE
E: ENOYL-COA HYDRATASE
F: ENOYL-COA HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,12012
Polymers168,4766
Non-polymers5,6446
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41070 Å2
ΔGint-300 kcal/mol
Surface area51090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.748, 145.286, 78.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Details6-subunits (A-F) come together as a dimer of trimers, forming a homo-hexamer, which is the biologically active form.

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Components

#1: Protein
ENOYL-COA HYDRATASE / / CROTONASE


Mass: 28079.285 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / Plasmid: PET20B(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P14604, enoyl-CoA hydratase
#2: Chemical
ChemComp-DAK / 4-(N,N-DIMETHYLAMINO)CINNAMOYL-COA


Mass: 940.745 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C32H47N8O17P3S
Details: DAC-CoA was synthesized as described in [D'Ordine et al., (1994) Biochem. 33, 12635]
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.41 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 8% PEG 4000, 100 mM sodium acetate, 75 mM sodium phosphate, 100 mM NaCl, 3 mM sodium azide, 3.5 mM DAC-CoA, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 %PEG40001reservoir
20.1 M1reservoirNaOAc
375 mMsodium phosphate1reservoirpH7.3
43.5 mMprotein1drop
575 mMsodium phosphate1drop
6100 mM1dropNaCl
73 mMsodium azide1droppH7.3

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Data collection

DiffractionMean temperature: 275 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 21, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. all: 65075 / Num. obs: 65075 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 11.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.64 % / Rmerge(I) obs: 0.413 / Num. unique all: 5554 / % possible all: 77.1
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 95 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: 1dub

1dub


Resolution: 2.3→35 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: protein_rep.param / Details: maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.22 6589 -RANDOM 10%
Rwork0.181 ---
all0.184 65075 --
obs0.184 65075 94.8 %-
Refinement stepCycle: LAST / Resolution: 2.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11790 0 366 486 12642
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.19
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.73
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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