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- PDB-1xl8: Crystal structure of mouse carnitine octanoyltransferase in compl... -

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Basic information

Entry
Database: PDB / ID: 1xl8
TitleCrystal structure of mouse carnitine octanoyltransferase in complex with octanoylcarnitine
ComponentsPeroxisomal carnitine O-octanoyltransferase
KeywordsTRANSFERASE / carnitine / octanoyltransferase / octanoylcarnitine
Function / homology
Function and homology information


Beta-oxidation of pristanoyl-CoA / carnitine O-octanoyltransferase / carnitine O-octanoyltransferase activity / medium-chain fatty acid metabolic process / carnitine metabolic process / Peroxisomal protein import / coenzyme A metabolic process / fatty acid beta-oxidation / fatty acid transport / generation of precursor metabolites and energy ...Beta-oxidation of pristanoyl-CoA / carnitine O-octanoyltransferase / carnitine O-octanoyltransferase activity / medium-chain fatty acid metabolic process / carnitine metabolic process / Peroxisomal protein import / coenzyme A metabolic process / fatty acid beta-oxidation / fatty acid transport / generation of precursor metabolites and energy / fatty acid metabolic process / peroxisome / response to xenobiotic stimulus / mitochondrion
Similarity search - Function
Choline/Carnitine o-acyltransferase / Carnitine o-acyltransferase, N-terminal / Choline/Carnitine o-acyltransferase, domain 2 / Acyltransferase ChoActase/COT/CPT / Choline/carnitine acyltransferase domain / Choline/Carnitine o-acyltransferase, domain 2 / Choline/Carnitine o-acyltransferase / Acyltransferases ChoActase / COT / CPT family signature 1. / Acyltransferases ChoActase / COT / CPT family signature 2. / Chloramphenicol Acetyltransferase ...Choline/Carnitine o-acyltransferase / Carnitine o-acyltransferase, N-terminal / Choline/Carnitine o-acyltransferase, domain 2 / Acyltransferase ChoActase/COT/CPT / Choline/carnitine acyltransferase domain / Choline/Carnitine o-acyltransferase, domain 2 / Choline/Carnitine o-acyltransferase / Acyltransferases ChoActase / COT / CPT family signature 1. / Acyltransferases ChoActase / COT / CPT family signature 2. / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Fumarase C; Chain B, domain 1 / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CARNITINE / OCTANOYLCARNITINE / Peroxisomal carnitine O-octanoyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJogl, G. / Hsiao, Y.S. / Tong, L.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of mouse carnitine octanoyltransferase and molecular determinants of substrate selectivity.
Authors: Jogl, G. / Hsiao, Y.S. / Tong, L.
History
DepositionSep 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisomal carnitine O-octanoyltransferase
B: Peroxisomal carnitine O-octanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,3519
Polymers142,3092
Non-polymers1,0417
Water7,458414
1
A: Peroxisomal carnitine O-octanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3172
Polymers71,1551
Non-polymers1621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisomal carnitine O-octanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0347
Polymers71,1551
Non-polymers8796
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.610, 163.610, 159.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Peroxisomal carnitine O-octanoyltransferase / COT


Mass: 71154.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crot, Cot / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3
References: UniProt: Q9DC50, carnitine O-octanoyltransferase
#2: Chemical ChemComp-152 / CARNITINE / (3-CARBOXY-2-(R)-HYDROXY-PROPYL)-TRIMETHYL-AMMONIUM


Mass: 162.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16NO3
#3: Chemical ChemComp-OCB / OCTANOYLCARNITINE / 3-CARBOXY-N,N,N-TRIMETHYL-2-(OCTANOYLOXY)PROPAN-1-AMINIUM


Mass: 288.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30NO4
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O
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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 100mM Hepes, 62%v/vMPD, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 80628 / Num. obs: 80628 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.9 Å2
Reflection shellResolution: 2.2→2.28 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XL7

1xl7


Resolution: 2.2→29.09 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 224973.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 5806 7.5 %RANDOM
Rwork0.199 ---
obs0.199 76996 95.2 %-
all-80628 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.1237 Å2 / ksol: 0.341071 e/Å3
Displacement parametersBiso mean: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å23.32 Å20 Å2
2--1.98 Å20 Å2
3----3.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9633 0 31 454 10118
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 884 7.4 %
Rwork0.255 11104 -
obs--88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMMPD.TOP
X-RAY DIFFRACTION3MPD.PARCAR.TOP
X-RAY DIFFRACTION4CAR.PAROCA.TOP
X-RAY DIFFRACTION5OCA.PARWATER.TO

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