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Basic information

Entry
Database: PDB / ID: 2iby
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
COENZYME A / : / Acetyl-CoA acetyltransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 12, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)169,94419
Polymers166,1964
Non-polymers3,74815
Water20,9331162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21040 Å2
ΔGint-107 kcal/mol
Surface area51220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.349, 106.746, 101.660
Angle α, β, γ (deg.)90.00, 103.06, 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

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Protein , 1 types, 4 molecules ABCD

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


Mass: 41549.047 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

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Non-polymers , 6 types, 1177 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1162 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.78 %
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: ESRF / Beamline: ID23-1 / Wavelength: 1.07225 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2006 / Details: mirrors
RadiationMonochromator: carved in a single Silicon (111) crystal whith a channel in the middle, called channel-cut design
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07225 Å / Relative weight: 1
ReflectionResolution: 1.85→73.32 Å / Num. all: 133490 / Num. obs: 133365 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 13.7
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 4.6 / Num. unique all: 19414 / Rsym value: 0.324 / % possible all: 100

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Processing

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

1wl4


Resolution: 1.85→73.32 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.547 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.129 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20312 6668 5 %RANDOM
Rwork0.16411 ---
obs0.16607 126697 100 %-
all-133365 --
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: 25.388 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.21 Å2
2--0.02 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.85→73.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11522 0 224 1162 12908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02212015
X-RAY DIFFRACTIONr_angle_refined_deg1.3052.00116304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.075.0511572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.29825.931403
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.462152115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0751536
X-RAY DIFFRACTIONr_chiral_restr0.0870.21949
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028604
X-RAY DIFFRACTIONr_nbd_refined0.2080.26282
X-RAY DIFFRACTIONr_nbtor_refined0.2970.28455
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.21163
X-RAY DIFFRACTIONr_metal_ion_refined0.0580.214
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.235
X-RAY DIFFRACTIONr_mcbond_it1.34137787
X-RAY DIFFRACTIONr_mcangle_it1.995412543
X-RAY DIFFRACTIONr_scbond_it1.59534268
X-RAY DIFFRACTIONr_scangle_it2.22743761
LS refinement shellResolution: 1.85→1.915 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.241 652 -
Rwork0.199 12390 -
obs-12390 100 %

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