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- PDB-2ib7: Crystallographic and kinetic studies of human mitochondrial aceto... -

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Basic information

Entry
Database: PDB / ID: 2ib7
TitleCrystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase (T2): the importance of potassium and chloride for its structure and function
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / thiolase fold / potassium ion / chloride / beta-alpha-beta-alpha-beta-alpha-beta-beta topology / alpha-beta-alpha-beta-alpha layered structure
Function / homology
Function and homology information


C-acetyltransferase activity / metanephric proximal convoluted tubule development / propionyl-CoA biosynthetic process / Beta-ketothiolase deficiency / Utilization of Ketone Bodies / Synthesis of Ketone Bodies / cholesterol O-acyltransferase activity / ketone body metabolic process / ketone body catabolic process / acetyl-CoA catabolic process ...C-acetyltransferase activity / metanephric proximal convoluted tubule development / propionyl-CoA biosynthetic process / Beta-ketothiolase deficiency / Utilization of Ketone Bodies / Synthesis of Ketone Bodies / cholesterol O-acyltransferase activity / ketone body metabolic process / ketone body catabolic process / acetyl-CoA catabolic process / acetyl-CoA C-acetyltransferase / L-isoleucine catabolic process / coenzyme A binding / Maturation of TCA enzymes and regulation of TCA cycle / acetyl-CoA C-acetyltransferase activity / acetyl-CoA biosynthetic process / Branched-chain amino acid catabolism / coenzyme A metabolic process / coenzyme A biosynthetic process / response to starvation / fatty acid beta-oxidation / potassium ion binding / adipose tissue development / response to hormone / Mitochondrial protein degradation / liver development / mitochondrial matrix / enzyme binding / endoplasmic reticulum / mitochondrion / extracellular exosome / identical protein binding
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal ...Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetyl-CoA acetyltransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHaapalainen, A.M. / Wierenga, R.K.
CitationJournal: Biochemistry / Year: 2007
Title: Crystallographic and Kinetic Studies of Human Mitochondrial Acetoacetyl-CoA Thiolase: The Importance of Potassium and Chloride Ions for Its Structure and Function
Authors: Haapalainen, A.M. / Merilainen, G. / Pirila, P.L. / Kondo, N. / Fukao, T. / Wierenga, R.K.
History
DepositionSep 11, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_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 1.4Oct 25, 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: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
C: Acetyl-CoA acetyltransferase
D: Acetyl-CoA acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,51517
Polymers166,1324
Non-polymers1,38313
Water16,286904
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17300 Å2
ΔGint-112 kcal/mol
Surface area51560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.257, 106.493, 101.734
Angle α, β, γ (deg.)90.00, 102.95, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit consists of one biological unit, the homotetramer

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Components

#1: Protein
Acetyl-CoA acetyltransferase / Acetoacetyl-CoA thiolase / T2


Mass: 41533.047 Da / Num. of mol.: 4 / Mutation: V34A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: liver / Gene: ACAT1 / Plasmid: pET3D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P24752, acetyl-CoA C-acetyltransferase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 904 / 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: 2.39 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 5000 monomethylether, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8125 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 17, 2005 / Details: mirrors
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8125 Å / Relative weight: 1
ReflectionResolution: 2.05→73.32 Å / Num. all: 98026 / Num. obs: 97946 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 14.8
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.2 / Num. unique all: 14142 / Rsym value: 0.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WL4

1wl4


Resolution: 2.05→73.32 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.717 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.178 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19803 4898 5 %RANDOM
Rwork0.15743 ---
obs0.15948 93047 100 %-
all-97945 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.507 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å2-0.05 Å2
2--0.34 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.05→73.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11512 0 82 904 12498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211808
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.98515981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69951563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.27325.9400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.531152099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6821536
X-RAY DIFFRACTIONr_chiral_restr0.0890.21904
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028516
X-RAY DIFFRACTIONr_nbd_refined0.20.25923
X-RAY DIFFRACTIONr_nbtor_refined0.2960.28261
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2955
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.218
X-RAY DIFFRACTIONr_mcbond_it1.49638047
X-RAY DIFFRACTIONr_mcangle_it2.091412495
X-RAY DIFFRACTIONr_scbond_it1.61434266
X-RAY DIFFRACTIONr_scangle_it2.23743486
LS refinement shellResolution: 2.05→2.122 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.247 478 -
Rwork0.184 9080 -
obs-9080 100 %

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