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Entry
Database: PDB / ID: 8bit
TitleCrystal structure of acyl-CoA synthetase from Metallosphaera sedula in complex with Coenzyme A and acetyl-AMP
Components4-hydroxybutyrate--CoA ligase 1
KeywordsLIGASE / CoA-ligase / acyl-CoA ligase / acetyl-CoA ligase / Thermostable ligase / Thermostable / Acetyl-AMP / substrate bound / monomer
Function / homology
Function and homology information


4-hydroxybutyrate-CoA ligase (AMP-forming) / medium-chain acyl-CoA ligase / propionate-CoA ligase / propionate-CoA ligase activity / medium-chain fatty acid-CoA ligase activity / acetate-CoA ligase / acetate-CoA ligase activity / fatty-acyl-CoA synthase activity / acyl-CoA metabolic process / fatty acid biosynthetic process ...4-hydroxybutyrate-CoA ligase (AMP-forming) / medium-chain acyl-CoA ligase / propionate-CoA ligase / propionate-CoA ligase activity / medium-chain fatty acid-CoA ligase activity / acetate-CoA ligase / acetate-CoA ligase activity / fatty-acyl-CoA synthase activity / acyl-CoA metabolic process / fatty acid biosynthetic process / ATP binding / membrane
Similarity search - Function
: / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Chem-6R9 / COENZYME A / 4-hydroxybutyrate--CoA ligase 1
Similarity search - Component
Biological speciesMetallosphaera sedula DSM 5348 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsCapra, N. / Thunnissen, A.M.W.H. / Janssen, D.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Front Catal / Year: 2024
Title: Adapting an acyl CoA ligase from Metallosphaera sedula for lactam formation by structure-guided protein engineering
Authors: Capra, N. / Lelievre, C. / Toure, O. / Fossey-Jouenne, A. / Vergne-Vaxelaire, C. / Janssen, D.B. / Thunnissen, A.M.W.H. / Zaparucha, A.
History
DepositionNov 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 2.0Feb 14, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _entity.formula_weight / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_strand_id / _entity_poly_seq.mon_id / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_peptide_omega.omega / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R_Free / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _reflns.d_resolution_low / _reflns.pdbx_number_measured_all / _software.classification / _software.name / _software.version / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_ref.pdbx_align_begin / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Description: Atomic clashes / Details: Removed link between Lys256 and Cys299 / Provider: author / Type: Coordinate replacement
Revision 2.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 4-hydroxybutyrate--CoA ligase 1
A: 4-hydroxybutyrate--CoA ligase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,7636
Polymers130,4492
Non-polymers2,3144
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.806, 93.190, 131.685
Angle α, β, γ (deg.)90.00, 91.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 4-hydroxybutyrate--CoA ligase 1 / Acetate--CoA ligase / Butyrate--CoA ligase / Propionate--CoA ligase


Mass: 65224.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Metallosphaera sedula DSM 5348 (archaea)
Strain: ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2 / Gene: Msed_0406 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CodonPlus RIPL
References: UniProt: A4YDT1, 4-hydroxybutyrate-CoA ligase (AMP-forming), acetate-CoA ligase, medium-chain acyl-CoA ligase, propionate-CoA ligase
#2: Chemical ChemComp-6R9 / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate


Mass: 389.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: Protein solution(~3 mg/ml) was mixed to a final volume of 1 uL in 1:1 ratio with reservoir solution containing 0.1M acetate pH 5.2, 0.2M NaCl, 6-8% PEG 1500.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.1→52.95 Å / Num. obs: 23358 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.981 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.132 / Rrim(I) all: 0.246 / Χ2: 0.95 / Net I/σ(I): 4.2
Reflection shellResolution: 3.1→3.31 Å / % possible obs: 99.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 1.132 / Num. measured all: 14154 / Num. unique obs: 4194 / CC1/2: 0.735 / Rpim(I) all: 0.728 / Rrim(I) all: 1.35 / Χ2: 0.98 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B7W

3b7w


Resolution: 3.1→52.95 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.903 / SU B: 86.567 / SU ML: 0.608 / Cross valid method: THROUGHOUT / ESU R Free: 0.564 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27664 1249 5.4 %RANDOM
Rwork0.21032 ---
obs0.21387 22090 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.011 Å2
Baniso -1Baniso -2Baniso -3
1-3.21 Å2-0 Å21.21 Å2
2--0.17 Å20 Å2
3----3.42 Å2
Refinement stepCycle: 1 / Resolution: 3.1→52.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9039 0 148 0 9187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0129402
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168955
X-RAY DIFFRACTIONr_angle_refined_deg21.85412731
X-RAY DIFFRACTIONr_angle_other_deg0.6451.76820666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.83951122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.672574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.523101664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.21396
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022151
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_it4.4014.3284494
X-RAY DIFFRACTIONr_mcbond_other4.44.3284494
X-RAY DIFFRACTIONr_mcangle_it6.9247.7765614
X-RAY DIFFRACTIONr_mcangle_other6.9247.7765615
X-RAY DIFFRACTIONr_scbond_it5.2494.8184908
X-RAY DIFFRACTIONr_scbond_other5.2484.8194909
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.48.6867118
X-RAY DIFFRACTIONr_long_range_B_refined12.87954.1440546
X-RAY DIFFRACTIONr_long_range_B_other12.87954.1440547
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 88 -
Rwork0.385 1609 -
obs--99.65 %
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)
11.17820.1013-0.16360.9431-0.31132.34560.0095-0.1172-0.0124-0.12110.0284-0.1897-0.2160.6596-0.03790.27270.01740.12920.7762-0.0570.087925.798558.122918.0238
21.6002-0.1825-0.36451.1522-0.34183.63170.0653-0.0837-0.14310.13720.07580.1966-0.174-0.5866-0.14110.2320.16780.08720.41420.07290.06732.382414.226746.3235
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B8 - 602
2X-RAY DIFFRACTION2A8 - 602

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