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- PDB-1nm8: Structure of Human Carnitine Acetyltransferase: Molecular Basis f... -

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Basic information

Entry
Database: PDB / ID: 1nm8
TitleStructure of Human Carnitine Acetyltransferase: Molecular Basis for Fatty Acyl Transfer
ComponentsCarnitine O-acetyltransferase
KeywordsTRANSFERASE / TWO equally sized domains / ANTI-PARALLEL BETA-STRAND
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 / fatty acid beta-oxidation using acyl-CoA oxidase / short-chain fatty acid metabolic process / 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 / fatty acid beta-oxidation using acyl-CoA oxidase / short-chain fatty acid metabolic process / 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 / Chloramphenicol acetyltransferase-like domain / 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 / Chloramphenicol acetyltransferase-like domain / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Carnitine O-acetyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsWu, D. / Govindasamy, L. / Lian, W. / Gu, Y. / Kukar, T. / Agbandje-McKenna, M. / McKenna, R.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure of Human Carnitine Acetyltransferase. Molecular Basis for Fatty Acyl Transfer
Authors: Wu, D. / Govindasamy, L. / Lian, W. / Gu, Y. / Kukar, T. / Agbandje-McKenna, M. / McKenna, R.
History
DepositionJan 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carnitine O-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)69,9031
Polymers69,9031
Non-polymers00
Water8,503472
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.500, 84.500, 57.500
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 O-acetyltransferase / Carnitine acetylase / CAT


Mass: 69902.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRAT OR CAT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P43155, carnitine O-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3948.49
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2951vapor diffusion, hanging drop6.2Bis-Tris, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
2vapor diffusion, hanging dropNaCl, VAPOR DIFFUSION, HANGING DROP
3vapor diffusion, hanging dropPEG 8000, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Details: Lian, W., (2002) Acta Crystallogr., D58, 1193.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlenzyme1drop
250 mMBis-Tris1reservoirpH6.2
3100 mM1reservoirNaCl
412-15 %PEG80001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONCHESS F220.9794, 0.9791, 0.9641
Detector
TypeIDDetectorDetails
RIGAKU RAXIS IV1IMAGE PLATEOSMIC mirrors
ADSC QUANTUM 42CCD
RadiationMonochromator: MONOGRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97941
30.97911
40.96411
ReflectionResolution: 1.6→50 Å / Num. all: 80622 / % possible obs: 90.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.043
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 80622 / Num. measured all: 724938
Reflection shell
*PLUS
Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.232 3914
Rwork0.208 -
all-724938
obs-80597
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4714 0 0 472 5186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.255
X-RAY DIFFRACTIONc_angle_d0.0051
Refinement
*PLUS
Lowest resolution: 50 Å / Num. reflection obs: 77731 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d

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