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- PDB-1dub: 2-ENOYL-COA HYDRATASE, DATA COLLECTED AT 100 K, PH 6.5 -

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Basic information

Entry
Database: PDB / ID: 1dub
Title2-ENOYL-COA HYDRATASE, DATA COLLECTED AT 100 K, PH 6.5
Components2-ENOYL-COA HYDRATASE
KeywordsLYASE / BETA-OXIDATION / COA / CROTONASE / ENOYL-COA HYDRATASE / FATTY ACID METABOLISM
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
ACETOACETYL-COENZYME A / Enoyl-CoA hydratase, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsWierenga, R.K. / Engel, C.K.
Citation
Journal: EMBO J. / Year: 1996
Title: Crystal structure of enoyl-coenzyme A (CoA) hydratase at 2.5 angstroms resolution: a spiral fold defines the CoA-binding pocket.
Authors: Engel, C.K. / Mathieu, M. / Zeelen, J.P. / Hiltunen, J.K. / Wierenga, R.K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Crystallization Experiments with 2-Enoyl-Coa Hydratase, Using an Automated 'Fast Screening Crystallization Protocol
Authors: Zeelen, J.P. / Hiltunen, J.K. / Wierenga, R.K.
History
DepositionJun 10, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: 2-ENOYL-COA HYDRATASE
B: 2-ENOYL-COA HYDRATASE
C: 2-ENOYL-COA HYDRATASE
D: 2-ENOYL-COA HYDRATASE
E: 2-ENOYL-COA HYDRATASE
F: 2-ENOYL-COA HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,18711
Polymers169,9296
Non-polymers4,2585
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32790 Å2
ΔGint-184 kcal/mol
Surface area52650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.972, 93.635, 246.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
2-ENOYL-COA HYDRATASE / CROTONASE / ENOYL-COA HYDRATASE 1


Mass: 28321.514 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: LIVER / References: UniProt: P14604, enoyl-CoA hydratase
#2: Chemical
ChemComp-CAA / ACETOACETYL-COENZYME A / Acetoacetyl-CoA


Mass: 851.607 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: (3S)-3-HYDROXYACYL-COA = TRANS-2 -ENOYL-COA + H(2)O. SUBCELLULAR LOCATION: ...CATALYTIC ACTIVITY: (3S)-3-HYDROXYACYL-COA = TRANS-2 -ENOYL-COA + H(2)O. SUBCELLULAR LOCATION: MITOCHONDRIAL MATRIX.
Nonpolymer detailsACETOACETYL-COA IS THE MOST EFFECTIVE INHIBITOR OF THE ENOYL-COA HYDRATASE REACTION THAT IS DESCRIBED.
Sequence detailsA 29 AMINO ACID N-TERMINAL LEADING SEQUENCE OF THE PROTEIN IS CLEAVED OFF UPON IMPORT INTO THE ...A 29 AMINO ACID N-TERMINAL LEADING SEQUENCE OF THE PROTEIN IS CLEAVED OFF UPON IMPORT INTO THE MITOCHONDRION. THE RESIDUE NUMBERING SCHEME IS ADAPTED FROM THE GENE SEQUENCE AND STARTS THEREFORE WITH GLY 30.

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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: 2.59 Å3/Da / Density % sol: 53 %
Crystal growpH: 6.5
Details: 100 MM MES/NAOH PH 6.5, 2.5 M AMMONIUM SULFATE, 10% OCTANOL, 1 MM DTT, 1 MM EDTA, 1 MM NA-AZIDE, 1 MM ACETOACETYL-COA.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mMprotein1drop
21.05-1.25 Mammonium sulfate1drop
350 mMMES1drop
40.5 mMDTT1drop
50.5 mM1dropNaN3
60.5 mMEDTA1drop
72.5 %(v/v)n-octanol1drop
82.1-2.5 Mammonium sulfate1reservoir
9100 mMMES1reservoir
101 mMDTT1reservoir
111 mM1reservoirNaN3
121 mMEDTA1reservoir
135 %(v/v)n-octanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.857
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 14, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.857 Å / Relative weight: 1
ReflectionResolution: 2.5→28.6 Å / Num. obs: 58197 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 22.77 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.6 / % possible all: 97.8
Reflection
*PLUS
Num. measured all: 243398

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.1refinement
DENZOdata reduction
RefinementMethod to determine structure: MIR / Resolution: 2.5→8 Å / Cross valid method: R-FREE / σ(F): 0
Details: ONLY 5 OF THE 6 SUBUNITS IN THE ASYMMETRIC UNIT HAVE A LIGAND BOUND. IN THE BINDING SITE OF SUBUNIT D A CLASH OF THE 3'-PHOSPHATE OF ACETO-ACETYL-COA WITH THE LOOP LYS 41 TO SER 45 OF A ...Details: ONLY 5 OF THE 6 SUBUNITS IN THE ASYMMETRIC UNIT HAVE A LIGAND BOUND. IN THE BINDING SITE OF SUBUNIT D A CLASH OF THE 3'-PHOSPHATE OF ACETO-ACETYL-COA WITH THE LOOP LYS 41 TO SER 45 OF A CRYSTALLOGRAPHIC SYMMETRY RELATED D SUBUNITS PREVENTS THE LIGAND FROM BINDING.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1688 3 %X-PLOR
Rwork0.209 ---
obs0.209 58197 92.9 %-
Displacement parametersBiso mean: 21.05 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11836 0 270 595 12701
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.49
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
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDRms dev Biso (Å2)Rms dev position (Å)Weight Biso Weight position
11X-RAY DIFFRACTION3.90.081150
22X-RAY DIFFRACTION40.28150
33X-RAY DIFFRACTION6.50.271100
44X-RAY DIFFRACTION60.96110
LS refinement shellResolution: 2.5→2.61 Å
RfactorNum. reflection% reflection
Rfree0.338 223 3 %
Rwork0.269 7108 -
obs--94.5 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.49

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