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- PDB-3c5e: Crystal structure of human acyl-CoA synthetase medium-chain famil... -

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Basic information

Entry
Database: PDB / ID: 3c5e
TitleCrystal structure of human acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in complex with ATP
ComponentsAcyl-coenzyme A synthetase ACSM2A, mitochondrial precursor
KeywordsLIGASE / MIDDLE-CHAIN ACYL-COA SYNTHETASE / XENOBIOTIC/MEDIUM-CHAIN FATTY ACID-COA LIGASE / STRUCTURAL GENOMICS CONSORTIUM / SGC / ATP-BINDING / FATTY ACID METABOLISM / LIPID METABOLISM / MAGNESIUM / METAL-BINDING / MITOCHONDRION / NUCLEOTIDE-BINDING POLYMORPHISM / TRANSIT PEPTIDE
Function / homology
Function and homology information


decanoate-CoA ligase activity / Conjugation of salicylate with glycine / medium-chain acyl-CoA ligase / fatty acid ligase activity / benzoate-CoA ligase / benzoate-CoA ligase activity / medium-chain fatty-acyl-CoA metabolic process / medium-chain fatty acid-CoA ligase activity / fatty-acyl-CoA synthase activity / acyl-CoA metabolic process ...decanoate-CoA ligase activity / Conjugation of salicylate with glycine / medium-chain acyl-CoA ligase / fatty acid ligase activity / benzoate-CoA ligase / benzoate-CoA ligase activity / medium-chain fatty-acyl-CoA metabolic process / medium-chain fatty acid-CoA ligase activity / fatty-acyl-CoA synthase activity / acyl-CoA metabolic process / triglyceride homeostasis / Aspirin ADME / fatty acid biosynthetic process / glucose homeostasis / mitochondrial matrix / mitochondrion / ATP binding / metal ion binding
Similarity search - Function
: / ANL, N-terminal domain / ANL, C-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme ...: / ANL, N-terminal domain / ANL, C-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Unknown ligand / Acyl-coenzyme A synthetase ACSM2A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPilka, E.S. / Kochan, G.T. / Bhatia, C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural snapshots for the conformation-dependent catalysis by human medium-chain acyl-coenzyme A synthetase ACSM2A.
Authors: Kochan, G. / Pilka, E.S. / von Delft, F. / Oppermann, U. / Yue, W.W.
History
DepositionJan 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 20, 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.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-coenzyme A synthetase ACSM2A, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,17512
Polymers63,3351
Non-polymers84111
Water13,980776
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.700, 98.073, 120.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acyl-coenzyme A synthetase ACSM2A, mitochondrial precursor / Acyl-CoA synthetase medium-chain family member 2A / Middle-chain acyl-CoA synthetase 2A / Butyrate- ...Acyl-CoA synthetase medium-chain family member 2A / Middle-chain acyl-CoA synthetase 2A / Butyrate-CoA ligase 2A / Butyryl coenzyme A synthetase 2A


Mass: 63334.562 Da / Num. of mol.: 1 / Fragment: Residues 32-577 / Mutation: L64P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACSM2A, ACSM2, MACS2 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q08AH3, medium-chain acyl-CoA ligase

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Non-polymers , 7 types, 787 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 776 / 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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / pH: 5.5
Details: 17% PEG 10000, 0.1M Ammonium acetate, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97926
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 19, 2007
RadiationMonochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.6→51.3 Å / Num. obs: 84181 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.071 / Rsym value: 0.043 / Net I/σ(I): 11.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2 / Rsym value: 0.372 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B7W

3b7w


Resolution: 1.6→49 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.002 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ADDITIONAL DENSITY IN THE ACTIVE SITE, PROBABLY UNIDENTIFIED ENDOGENOUS SUBSTRATE, WAS MODELLED AS A SET OF UNL ATOMS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19423 4500 5.1 %RANDOM
Rwork0.15611 ---
obs0.15806 84181 99.46 %-
all-84181 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.104 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---1.05 Å20 Å2
3---1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4149 0 53 776 4978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224464
X-RAY DIFFRACTIONr_bond_other_d0.0010.023026
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.976105
X-RAY DIFFRACTIONr_angle_other_deg0.97937442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6355581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16524.516186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37215771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.491523
X-RAY DIFFRACTIONr_chiral_restr0.1070.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214958
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02865
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.57132757
X-RAY DIFFRACTIONr_mcbond_other0.79131111
X-RAY DIFFRACTIONr_mcangle_it3.84354488
X-RAY DIFFRACTIONr_scbond_it5.58671707
X-RAY DIFFRACTIONr_scangle_it7.869111597
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 321 -
Rwork0.252 5802 -
obs--93.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2620.0524-0.00880.3105-0.01690.16310.0056-0.021-0.00780.0149-0.0084-0.0228-0.0191-0.00990.0028-0.01060.00910.0101-0.0290.011-0.024224.2329-9.3454-17.8036
23.6618-1.7773-0.8331.38011.3611.9583-0.0051-0.41980.14330.1040.0790.17870.0231-0.1721-0.07390.03120.0064-0.0243-0.01950.0280.020827.4373-2.5875-14.9152
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA34 - 56927 - 562
2X-RAY DIFFRACTION2AB - F701 - 8041

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