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- PDB-7ky1: Molecular basis for control of antibiotic production by a bacteri... -

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Basic information

Entry
Database: PDB / ID: 7ky1
TitleMolecular basis for control of antibiotic production by a bacterial hormones
ComponentsTetR family transcriptional regulator
KeywordsANTIBIOTIC / streptomyces / tetR-family transcriptional regulator / signalling / microbial natural product
Function / homologyTetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / regulation of gene expression / DNA binding / identical protein binding / TetR family transcriptional regulator
Function and homology information
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.50003347687 Å
AuthorsBhukya, H. / Fulop, V.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Royal SocietyBB/M022765/1 United Kingdom
Royal SocietyUF090255 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M017982/1 United Kingdom
CitationJournal: Nature / Year: 2021
Title: Molecular basis for control of antibiotic production by a bacterial hormone.
Authors: Shanshan Zhou / Hussain Bhukya / Nicolas Malet / Peter J Harrison / Dean Rea / Matthew J Belousoff / Hariprasad Venugopal / Paulina K Sydor / Kathryn M Styles / Lijiang Song / Max J Cryle / ...Authors: Shanshan Zhou / Hussain Bhukya / Nicolas Malet / Peter J Harrison / Dean Rea / Matthew J Belousoff / Hariprasad Venugopal / Paulina K Sydor / Kathryn M Styles / Lijiang Song / Max J Cryle / Lona M Alkhalaf / Vilmos Fülöp / Gregory L Challis / Christophe Corre /
Abstract: Actinobacteria produce numerous antibiotics and other specialized metabolites that have important applications in medicine and agriculture. Diffusible hormones frequently control the production of ...Actinobacteria produce numerous antibiotics and other specialized metabolites that have important applications in medicine and agriculture. Diffusible hormones frequently control the production of such metabolites by binding TetR family transcriptional repressors (TFTRs), but the molecular basis for this remains unclear. The production of methylenomycin antibiotics in Streptomyces coelicolor A3(2) is initiated by the binding of 2-alkyl-4-hydroxymethylfuran-3-carboxylic acid (AHFCA) hormones to the TFTR MmfR. Here we report the X-ray crystal structure of an MmfR-AHFCA complex, establishing the structural basis for hormone recognition. We also elucidate the mechanism for DNA release upon hormone binding through the single-particle cryo-electron microscopy structure of an MmfR-operator complex. DNA binding and release assays with MmfR mutants and synthetic AHFCA analogues define the role of individual amino acid residues and hormone functional groups in ligand recognition and DNA release. These findings will facilitate the exploitation of actinobacterial hormones and their associated TFTRs in synthetic biology and in the discovery of new antibiotics.
History
DepositionDec 6, 2020Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 3, 2021ID: 6SRM
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TetR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)24,0231
Polymers24,0231
Non-polymers00
Water4,125229
1
A: TetR family transcriptional regulator

A: TetR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)48,0462
Polymers48,0462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Buried area2510 Å2
ΔGint-18 kcal/mol
Surface area16810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.500, 115.720, 53.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-390-

HOH

21A-451-

HOH

31A-495-

HOH

41A-527-

HOH

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Components

#1: Protein TetR family transcriptional regulator


Mass: 24023.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: mmfR / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JN89
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 1.93 Å3/Da / Density % sol: 36.3 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 10-15% PEG 3350 and 0.2-0.25 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 21, 2012 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→53.649 Å / Num. obs: 29976 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 19.2805422876 Å2 / CC1/2: 1 / Rsym value: 0.53 / Net I/σ(I): 16
Reflection shellResolution: 1.5→1.55 Å / Num. unique obs: 1256 / Rsym value: 0.659 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.50003347687→53.649 Å / SU ML: 0.210635969747 / Cross valid method: THROUGHOUT / σ(F): 1.34383303184 / Phase error: 25.734972964
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2131036866 1181 3.93981852148 %Random
Rwork0.188731914226 28795 --
obs0.189734709652 29976 99.0091161316 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.9459058009 Å2
Refinement stepCycle: LAST / Resolution: 1.50003347687→53.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1474 0 0 229 1703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006738723795461544
X-RAY DIFFRACTIONf_angle_d0.9241865217532097
X-RAY DIFFRACTIONf_chiral_restr0.0477286775768227
X-RAY DIFFRACTIONf_plane_restr0.00608817786258279
X-RAY DIFFRACTIONf_dihedral_angle_d12.7915073903947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.50003347687-1.56830.3589642019761340.3108117083083404X-RAY DIFFRACTION95.4153182309
1.5683-1.6510.2636675592191510.2511513392473582X-RAY DIFFRACTION99.7594869054
1.651-1.75440.2800502401221310.2231528235543601X-RAY DIFFRACTION99.7594226143
1.7544-1.88990.2278943213771400.2068881397723595X-RAY DIFFRACTION99.414426404
1.8899-2.08010.2444807230181500.2107014439523574X-RAY DIFFRACTION99.3331555081
2.0801-2.38110.2117930397631600.1797029723323600X-RAY DIFFRACTION99.4708994709
2.3811-2.99990.2112633602191590.1895886340773655X-RAY DIFFRACTION99.5302713987
2.9999-53.6490.1828286239811560.1634032718333784X-RAY DIFFRACTION99.3193849256
Refinement TLS params.Method: refined / Origin x: 13.7676516377 Å / Origin y: 42.5010146162 Å / Origin z: 35.3873381032 Å
111213212223313233
T0.122201482818 Å2-0.0235448911681 Å20.00523373646636 Å2-0.122643578091 Å2-0.00904901473757 Å2--0.115807836934 Å2
L0.166079151006 °2-0.0211537512577 °2-0.0865889396521 °2-0.716257590298 °2-0.718783235474 °2--0.434118945282 °2
S-0.0372730833509 Å °-0.0151451386189 Å °-0.0183869301178 Å °-0.112941452998 Å °0.114283879865 Å °-0.0124098320819 Å °0.0614151202353 Å °-0.126629298187 Å °0.0374886339348 Å °
Refinement TLS groupSelection details: all

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