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- PDB-3gpc: Crystal structure of human Acyl-CoA synthetase medium-chain famil... -

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Basic information

Entry
Database: PDB / ID: 3gpc
TitleCrystal structure of human Acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in a complex with CoA
ComponentsAcyl-coenzyme A synthetase ACSM2A
KeywordsLIGASE / MIDDLE-CHAIN ACYL-COA SYNTHETASE / XENOBIOTIC/MEDIUM-CHAIN FATTY ACID-COA LIGASE / ATP-BINDING / FATTY ACID METABOLISM / LIPID METABOLISM / MAGNESIUM / METAL-BINDING / MITOCHONDRION / NUCLEOTIDE-BINDING POLYMORPHISM / TRANSIT PEPTIDE / NUCLEOTIDE-BINDING
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 / acyl-CoA metabolic process / fatty-acyl-CoA synthase activity ...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 / acyl-CoA metabolic process / fatty-acyl-CoA synthase activity / triglyceride homeostasis / Aspirin ADME / fatty acid biosynthetic process / glucose homeostasis / mitochondrial matrix / mitochondrion / ATP binding / metal ion binding
Similarity search - Function
: / ANL, C-terminal domain / ANL, N-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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase ...: / ANL, C-terminal domain / ANL, N-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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Acyl-coenzyme A synthetase ACSM2A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPilka, E.S. / Kochan, G.T. / Yue, W.W. / 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
DepositionMar 23, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionApr 7, 2009ID: 3EYN
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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 / 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_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-coenzyme A synthetase ACSM2A
B: Acyl-coenzyme A synthetase ACSM2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2536
Polymers126,6692
Non-polymers1,5844
Water14,124784
1
A: Acyl-coenzyme A synthetase ACSM2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1263
Polymers63,3351
Non-polymers7922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acyl-coenzyme A synthetase ACSM2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1263
Polymers63,3351
Non-polymers7922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.604, 97.535, 118.210
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 63334.562 Da / Num. of mol.: 2 / Fragment: UNP residues 32-577 / Mutation: L64P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACSM2, ACSM2A, MACS2 / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): HIGH FIVE / References: UniProt: Q08AH3, medium-chain acyl-CoA ligase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 784 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMUCH OF THE COA PANTETHEINE MOIETY WAS DISORDERED AND NOT INCLUDED IN THE MODEL

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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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG3350, 0.20M (NH4)2SO4, 0.1M BIS-TRIS, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.5418 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 10, 2008
RadiationMonochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 77119 / Num. obs: 73279 / % possible obs: 77.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.074 / Rsym value: 0.053 / Net I/σ(I): 8.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.5 / Num. unique all: 11811 / Rsym value: 0.265 / % possible all: 81.7

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B7W

3b7w


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.797 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.171 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 3812 4.9 %RANDOM
Rwork0.16236 ---
obs0.16547 73279 77.63 %-
all-77119 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.683 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-0.17 Å2
2---0.89 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8200 0 83 784 9067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228598
X-RAY DIFFRACTIONr_bond_other_d0.0010.025766
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.97211725
X-RAY DIFFRACTIONr_angle_other_deg0.91314149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78751093
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84124.373343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.257151444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7761542
X-RAY DIFFRACTIONr_chiral_restr0.0950.21308
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219477
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021646
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_it2.70635360
X-RAY DIFFRACTIONr_mcbond_other0.82732170
X-RAY DIFFRACTIONr_mcangle_it3.98158666
X-RAY DIFFRACTIONr_scbond_it6.41673238
X-RAY DIFFRACTIONr_scangle_it8.779113044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 323 -
Rwork0.229 5636 -
obs--81.34 %
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)
10.21330.042-0.01650.2260.00820.283-0.0119-0.0103-0.00120.00550.02560.00270.0075-0.0109-0.01370.01850.01590.01080.0170.01030.007722.8494-15.515111.4147
20.2995-0.0349-0.05090.308-0.09970.16060.00630.02510.0133-0.032-0.0168-0.01740.0193-0.01490.01050.00730.00080.00330.00520.00210.0057-4.4306-44.576947.1566
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 569
2X-RAY DIFFRACTION2B35 - 569

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