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- PDB-8oqm: Structure of Mycobacterium tuberculosis beta-oxidation trifunctio... -

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Basic information

Entry
Database: PDB / ID: 8oqm
TitleStructure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with Fragment-M-10
Components
  • 3-hydroxyacyl-CoA dehydrogenase
  • Putative acyltransferase Rv0859
KeywordsOXIDOREDUCTASE / fatty acid beta oxidation complex / mycobacterium tuberculosis / TFE / fragment screening / substrate channeling
Function / homology
Function and homology information


long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / acetyl-CoA C-acetyltransferase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / peptidoglycan-based cell wall / plasma membrane / cytosol
Similarity search - Function
: / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site ...: / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / Thiolase-like / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / 6-azanyl-4-oxidanyl-naphthalene-2-sulfonic acid / Putative acyltransferase Rv0859 / Probable fatty oxidation protein FadB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDalwani, S. / Wierenga, R.K. / Venkatesan, R.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of Finland293369 Finland
Academy of Finland289024 Finland
Academy of Finland319194 Finland
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a ...Title: Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate-channeling path between them.
Authors: Dalwani, S. / Metz, A. / Huschmann, F.U. / Weiss, M.S. / Wierenga, R.K. / Venkatesan, R.
#1: Journal: Biorxiv / Year: 2024
Title: Crystallographic fragment binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a ...Title: Crystallographic fragment binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate channeling path between them
Authors: Dalwani, S. / Metz, A. / Huschmann, F.U. / Weiss, M.S. / Wierenga, R.K. / Venkatesan, R.
#2: Journal: J Struct Biol / Year: 2021
Title: Substrate specificity and conformational flexibility properties of the Mycobacterium tuberculosis beta-oxidation trifunctional enzyme.
Authors: Dalwani, S.
#3: Journal: ACS Chem Biol / Year: 2013
Title: Structure of mycobacterial beta-oxidation trifunctional enzyme reveals its altered assembly and putative substrate channeling pathway.
Authors: Venkatesan, R. / Wierenga, R.K.
History
DepositionApr 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 2.0Jul 24, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / pdbx_contact_author / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_asym / struct_conf / struct_mon_prot_cis
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_database_status.pdb_format_compatible / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_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.end_label_asym_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _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_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_length / _struct_mon_prot_cis.pdbx_omega_angle
Description: Model completeness
Details: Changes as suggested during the review process of article submission
Provider: author / Type: Coordinate replacement
Revision 2.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-hydroxyacyl-CoA dehydrogenase
B: 3-hydroxyacyl-CoA dehydrogenase
C: Putative acyltransferase Rv0859
D: Putative acyltransferase Rv0859
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,19429
Polymers240,9324
Non-polymers3,26225
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15970 Å2
ΔGint-251 kcal/mol
Surface area82530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)247.918, 134.911, 119.214
Angle α, β, γ (deg.)90.000, 110.622, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein 3-hydroxyacyl-CoA dehydrogenase


Mass: 78005.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: fadB, Rv0860 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53872, 3-hydroxyacyl-CoA dehydrogenase
#2: Protein Putative acyltransferase Rv0859


Mass: 42460.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: fadA, Rv0859 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53871, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 5 types, 75 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-A1IDU / 6-[(6-azanyl-4-oxidanyl-naphthalen-2-yl)sulfonylamino]-4-oxidanyl-naphthalene-2-sulfonic acid


Mass: 460.480 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H16N2O7S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-VWO / 6-azanyl-4-oxidanyl-naphthalene-2-sulfonic acid / 7-amino-1-naphthol-3-sulfonic acid


Mass: 239.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H9NO4S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.87 Å3/Da / Density % sol: 68.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2 M Ammonium Sulfate, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.968619 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968619 Å / Relative weight: 1
ReflectionResolution: 3.2→48.32 Å / Num. obs: 60500 / % possible obs: 99.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 94.92 Å2 / CC1/2: 0.986 / Net I/σ(I): 5.9
Reflection shellResolution: 3.2→3.28 Å / Num. unique obs: 4352 / CC1/2: 0.241

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.29 Å / SU ML: 0.4368 / Cross valid method: FREE R-VALUE / σ(F): 0.21 / Phase error: 25.6872
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2419 2884 4.8 %
Rwork0.2034 57203 -
obs0.2053 60087 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.5 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16657 0 191 50 16898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001617122
X-RAY DIFFRACTIONf_angle_d0.425623198
X-RAY DIFFRACTIONf_chiral_restr0.03942611
X-RAY DIFFRACTIONf_plane_restr0.00373069
X-RAY DIFFRACTIONf_dihedral_angle_d11.88486307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.250.37951240.34622385X-RAY DIFFRACTION88.13
3.25-3.310.37691450.31912626X-RAY DIFFRACTION95.68
3.31-3.370.33931460.30582685X-RAY DIFFRACTION98.44
3.37-3.430.34311130.28982745X-RAY DIFFRACTION99.2
3.43-3.50.32021450.28072742X-RAY DIFFRACTION99.83
3.5-3.580.27461400.27662711X-RAY DIFFRACTION99.82
3.58-3.660.33571600.26092746X-RAY DIFFRACTION99.93
3.66-3.750.29251230.24342776X-RAY DIFFRACTION99.9
3.75-3.850.26671340.222733X-RAY DIFFRACTION99.9
3.85-3.970.23771330.21012735X-RAY DIFFRACTION99.58
3.97-4.090.21281130.19542765X-RAY DIFFRACTION99.48
4.09-4.240.21551690.18262691X-RAY DIFFRACTION99.65
4.24-4.410.21911370.17682758X-RAY DIFFRACTION99.48
4.41-4.610.19011370.162724X-RAY DIFFRACTION99.62
4.61-4.850.18521370.16372750X-RAY DIFFRACTION99.76
4.85-5.160.22781280.16982784X-RAY DIFFRACTION99.86
5.16-5.560.23951280.17872746X-RAY DIFFRACTION99.97
5.56-6.110.23481500.19442767X-RAY DIFFRACTION99.9
6.11-70.21631530.20012764X-RAY DIFFRACTION99.62
7-8.80.20951380.16892759X-RAY DIFFRACTION99.72
8.81-48.290.23351310.19522811X-RAY DIFFRACTION98.49
Refinement TLS params.Method: refined / Origin x: -43.6776560804 Å / Origin y: 34.2838417797 Å / Origin z: -1.64694633128 Å
111213212223313233
T0.673693703061 Å2-0.00913109636239 Å20.0306601841923 Å2-0.634997107283 Å20.0026982419279 Å2--0.830258793918 Å2
L0.262767349289 °20.00764432241701 °2-0.0256612500347 °2-0.156733679389 °2-0.110614261111 °2--0.645167030774 °2
S0.00441551452764 Å °0.00990847032583 Å °-0.0101844078252 Å °-0.0175289988896 Å °0.00166735215056 Å °0.102727405158 Å °0.0158018257457 Å °-0.126848885155 Å °0.00392898126582 Å °
Refinement TLS groupSelection details: all

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