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- PDB-9jj9: Class 3 state of the GfsA KSQ-ancestralAT chimeric didomain in co... -

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Basic information

Entry
Database: PDB / ID: 9jj9
TitleClass 3 state of the GfsA KSQ-ancestralAT chimeric didomain in complex with the GfsA ACP domain
Components
  • Polyketide synthase
  • Polyketide synthase GfsA
KeywordsLYASE / decarboxylase / polyketide synthase
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Carboxy-lyases / secondary metabolite biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / lyase activity
Similarity search - Function
Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / : ...Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-9EF / Polyketide synthase GfsA
Similarity search - Component
Biological speciesStreptomyces graminofaciens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsChisuga, T. / Liao, Z. / Adachi, N. / Kawasaki, M. / Moriya, T. / Senda, T. / Kudo, F. / Eguchi, T. / Miyanaga, A.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H02911 Japan
Japan Society for the Promotion of Science (JSPS)23K19283 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Ancestral sequence reconstruction as a tool for structural analysis of modular polyketide synthases
Authors: Chisuga, T. / Takinami, S. / Liao, Z. / Karasawa, M. / Adachi, N. / Kawasaki, M. / Moriya, T. / Senda, T. / Terada, T. / Kudo, F. / Eguchi, T. / Nakano, S. / Ito, S. / Miyanaga, A.
History
DepositionSep 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Polyketide synthase GfsA
C: Polyketide synthase
A: Polyketide synthase GfsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,9944
Polymers136,6113
Non-polymers3831
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Polyketide synthase GfsA / FD-891 synthase GfsA / loading and modules 1 to 4


Mass: 63183.352 Da / Num. of mol.: 2 / Mutation: Q197C
Source method: isolated from a genetically manipulated source
Details: GfsA KSQ-ancestralAT / Source: (gene. exp.) Streptomyces graminofaciens (bacteria) / Gene: gfsA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E0D202, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Protein Polyketide synthase / acyl carrier protein


Mass: 10244.458 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces graminofaciens (bacteria) / Gene: gfsA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E0D202
#3: Chemical ChemComp-9EF / N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 383.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26N3O8P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Class 3 state of the GfsA KSQ-ancestralAT chimeric didomain in complex with the GfsA ACP domain
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Streptomyces graminofaciens (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
15 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES-NaOH1
250 mMsodium chlorideNaCl1
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105895 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0017858
ELECTRON MICROSCOPYf_angle_d0.38710683
ELECTRON MICROSCOPYf_dihedral_angle_d3.211134
ELECTRON MICROSCOPYf_chiral_restr0.0391230
ELECTRON MICROSCOPYf_plane_restr0.0041400

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