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- PDB-1s5o: Structural and Mutational Characterization of L-carnitine Binding... -

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Basic information

Entry
Database: PDB / ID: 1s5o
TitleStructural and Mutational Characterization of L-carnitine Binding to Human carnitine Acetyltransferase
Componentscarnitine acetyltransferase isoform 2
KeywordsTRANSFERASE / Carnitine acetyltransferase / binary complex / steady-state enzyme kinetics / substrate binding site
Function / homology
Function and homology information


carnitine O-acetyltransferase / carnitine O-acetyltransferase activity / Beta-oxidation of pristanoyl-CoA / carnitine O-octanoyltransferase / acyl-CoA oxidase activity / carnitine O-octanoyltransferase activity / carnitine metabolic process, CoA-linked / short-chain fatty acid metabolic process / fatty acid beta-oxidation using acyl-CoA oxidase / medium-chain fatty acid metabolic process ...carnitine O-acetyltransferase / carnitine O-acetyltransferase activity / Beta-oxidation of pristanoyl-CoA / carnitine O-octanoyltransferase / acyl-CoA oxidase activity / carnitine O-octanoyltransferase activity / carnitine metabolic process, CoA-linked / short-chain fatty acid metabolic process / fatty acid beta-oxidation using acyl-CoA oxidase / medium-chain fatty acid metabolic process / peroxisomal matrix / Peroxisomal protein import / peroxisome / mitochondrial inner membrane / endoplasmic reticulum / mitochondrion / cytosol
Similarity search - Function
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-like domain / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain superfamily ...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-like domain / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CARNITINE / Carnitine O-acetyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGovindasamy, L. / Kukar, T. / Lian, W. / Pedersen, B. / Gu, Y. / Agbandje-Mckenna, M. / Jin, S. / Mckenna, R. / Wu, D.
CitationJournal: J.Struct.Biol. / Year: 2004
Title: Structural and mutational characterization of l-carnitine binding to human carnitine acetyltransferase.
Authors: Govindasamy, L. / Kukar, T. / Lian, W. / Pedersen, B. / Gu, Y. / Agbandje-McKenna, M. / Jin, S. / McKenna, R. / Wu, D.
History
DepositionJan 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE AUTHORS STATE THE ELECTRON DENSITY MAP CONFIRMS THE THR RESIDUE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: carnitine acetyltransferase isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0652
Polymers69,9031
Non-polymers1621
Water8,377465
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.560, 84.650, 57.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein carnitine acetyltransferase isoform 2


Mass: 69902.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P43155, carnitine O-acetyltransferase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 48.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Bis-Tris, NaCl, PEG8000, L-Carnitine, hpCAT, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
21 mML-carnitine1drop
350 mMBis-Tris1reservoirpH6.2
4100 mM1reservoirNaCl
512-15 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9504 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9504 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 58948 / % possible obs: 91.6 % / Observed criterion σ(F): 4 / Rsym value: 0.086 / Net I/σ(I): 4.12
Reflection shellResolution: 1.8→1.86 Å / Num. unique all: 5280 / Rsym value: 0.343 / % possible all: 83.3
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 83.3 % / Rmerge(I) obs: 0.343

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
SHELXL-97refinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NM8

1nm8


Resolution: 1.8→50 Å / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rwork0.189 -
all0.223 58948
obs0.189 -
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4714 0 11 465 5190
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.3
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 5 / Rfactor Rfree: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.3

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