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- PDB-3eq6: Crystal structure of human acyl-CoA synthetase medium-chain famil... -

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Basic information

Entry
Database: PDB / ID: 3eq6
TitleCrystal structure of human acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in a ternary complex with products
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 / Structural Genomics / SGC / Structural Genomics Consortium
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 MONOPHOSPHATE / Butyryl Coenzyme A / Acyl-coenzyme A synthetase ACSM2A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPilka, E.S. / Kochan, G. / 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
DepositionSep 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 11, 2015Group: Non-polymer description
Revision 1.3Feb 3, 2016Group: Non-polymer description
Revision 1.4Nov 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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

Downloads & links

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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)129,0396
Polymers126,6692
Non-polymers2,3704
Water8,053447
1
A: Acyl-coenzyme A synthetase ACSM2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5193
Polymers63,3351
Non-polymers1,1852
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)64,5193
Polymers63,3351
Non-polymers1,1852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.028, 98.041, 116.660
Angle α, β, γ (deg.)90.00, 94.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 3 / Auth seq-ID: 37 - 569 / Label seq-ID: 30 - 562

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: ACSM2A / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): high five / References: UniProt: Q08AH3, medium-chain acyl-CoA ligase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-BCO / Butyryl Coenzyme A / S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} butanethioate (non-preferred name)


Mass: 837.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H42N7O17P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Mg(form), 15% PEG3350, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 4, 2008 / Details: OSMIC
RadiationMonochromator: NI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→24.99 Å / Num. all: 49866 / Num. obs: 47300 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.107 / Rsym value: 0.07 / Net I/σ(I): 8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7167 / Rsym value: 0.323 / % possible all: 98

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0055refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B7W

3b7w


Resolution: 2.4→21.73 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 15.136 / SU ML: 0.161 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.394 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23638 2531 5.1 %RANDOM
Rwork0.18674 ---
obs0.18928 47300 99.41 %-
all-49866 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å2-1.79 Å2
2---1.5 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.4→21.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8225 0 152 447 8824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228610
X-RAY DIFFRACTIONr_bond_other_d0.0020.025765
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9811732
X-RAY DIFFRACTIONr_angle_other_deg0.944314119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21351072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23324.327342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.624151422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5031542
X-RAY DIFFRACTIONr_chiral_restr0.0920.21308
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219457
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021661
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_it2.33535321
X-RAY DIFFRACTIONr_mcbond_other0.39832157
X-RAY DIFFRACTIONr_mcangle_it3.84958598
X-RAY DIFFRACTIONr_scbond_it6.62573289
X-RAY DIFFRACTIONr_scangle_it8.481113131
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
3108tight positional0.040.05
3753loose positional0.045
3108tight thermal0.210.5
3753loose thermal0.1610
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 175 -
Rwork0.248 3412 -
obs--97.63 %
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)
10.536-0.07650.1860.83370.05220.29910.0142-0.00310.0219-0.06220.00230.02470.03180.0115-0.01640.0120.00310.00440.00980.00720.0399-10.665720.0156-9.558
20.2640.18150.3640.58660.21211.0020.0102-0.0611-0.0257-0.00140.00140.02740.0574-0.1339-0.01150.11940.0154-0.00490.1335-0.00180.074-25.271664.3438-43.9493
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 569
2X-RAY DIFFRACTION2B37 - 569

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