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- PDB-2h3w: Crystal structure of the S554A/M564G mutant of murine carnitine a... -

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Basic information

Entry
Database: PDB / ID: 2h3w
TitleCrystal structure of the S554A/M564G mutant of murine carnitine acetyltransferase in complex with hexanoylcarnitine and CoA
Componentscarnitine acetyltransferase
KeywordsTRANSFERASE / carnitine acyltransferase
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 protein import / fatty acid metabolic process / peroxisome / mitochondrial inner membrane / endoplasmic reticulum / mitochondrion
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
COENZYME A / Chem-HC5 / Carnitine O-acetyltransferase / Carnitine O-acetyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHsiao, Y.S. / Jogl, G. / Tong, L.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal structures of murine carnitine acetyltransferase in ternary complexes with its substrates
Authors: Hsiao, Y.-S. / Jogl, G. / Tong, L.
History
DepositionMay 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: carnitine acetyltransferase
B: carnitine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,9516
Polymers135,8952
Non-polymers2,0564
Water27,0231500
1
A: carnitine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9763
Polymers67,9481
Non-polymers1,0282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: carnitine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9763
Polymers67,9481
Non-polymers1,0282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.060, 89.070, 122.780
Angle α, β, γ (deg.)90.00, 128.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein carnitine acetyltransferase


Mass: 67947.742 Da / Num. of mol.: 2 / Fragment: Residues 30-625 / Mutation: S554A:M564G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crat / Production host: Escherichia coli (E. coli) / References: UniProt: Q3V1Y3, UniProt: P47934*PLUS
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-HC5 / (R)-3-CARBOXY-2-(HEXANOYLOXY)-N,N,N-TRIMETHYLPROPAN-1-AMINIUM / HEXANOYLCARNITINE


Mass: 260.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1500 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris, 18% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9798
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 76084 / % possible obs: 94.1 % / Redundancy: 3 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 22.3494
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.108 / Mean I/σ(I) obs: 6.515 / % possible all: 77.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBTHEN SOLVE/RESOLVEphasing
CNS1.1refinement
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.91 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 377280.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 5768 7.6 %RANDOM
Rwork0.177 ---
all0.177 ---
obs0.177 75758 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.9734 Å2 / ksol: 0.340981 e/Å3
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.33 Å20 Å2-0.21 Å2
2---2.41 Å20 Å2
3----2.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9552 0 132 1500 11184
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.255 478 7.5 %
Rwork0.211 5912 -
obs--79.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2oca.parhca.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5coa.parcoa.top

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