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- PDB-9vbt: Cryo-EM structure of the multi-component acyltransferase complex ... -

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Basic information

Entry
Database: PDB / ID: 9vbt
TitleCryo-EM structure of the multi-component acyltransferase complex MucABC from Streptococcus macacae at a stoichiometric ratio of 4:4:4
Components
  • 2,4-diacetylphloroglucinol biosynthesis protein PhlB family protein
  • 3-oxoacyl-[acyl-carrier-protein (ACP)] synthase III domain protein
  • 3-oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal domain protein
KeywordsTRANSFERASE / enzyme complex / thiolase / Friedel-Crafts acylation / biosynthesis
Function / homology
Function and homology information


secondary metabolite biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / acyltransferase activity
Similarity search - Function
Domain of unknown function DUF35, rubredoxin-like zinc ribbon domain, N-terminal / : / ChsH2, rubredoxin-like zinc ribbon domain / : / Thiolase C-terminal domain-like / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase / Thiolase-like / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
2,4-diacetylphloroglucinol biosynthesis protein PhlB family protein / 3-oxoacyl-[acyl-carrier-protein (ACP)] synthase III domain protein / 3-oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal domain protein
Similarity search - Component
Biological speciesStreptococcus macacae NCTC 11558 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.32 Å
AuthorsLuo, Z. / Shen, Z. / Liao, G. / Tang, X. / Pan, X.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32322039 China
National Natural Science Foundation of China (NSFC)32401633 China
National Natural Science Foundation of China (NSFC)82173719 China
CitationJournal: Nat Commun / Year: 2026
Title: Evolutionary repurposing of a metabolic thiolase complex enables antibiotic biosynthesis.
Authors: Ge Liao / Ruolan Sun / Zilin Shen / Zhiteng Luo / Cuiping Pang / Zhuanglin Shen / Anfu Wei / Chengneng Mi / Gengfan Wu / Fengfang Li / Yong-Xin Li / Kin Kuan Hoi / Xiaojing Pan / Xiaoyu Tang /
Abstract: The functional diversification of biosynthetic enzymes underlies the chemical richness of natural products, yet how primary metabolic enzymes evolve to acquire specialized functions in secondary ...The functional diversification of biosynthetic enzymes underlies the chemical richness of natural products, yet how primary metabolic enzymes evolve to acquire specialized functions in secondary metabolism remains elusive. Here, we report a tripartite enzyme complex from oral Streptococcus species-comprising 3-hydroxy-3-methylglutaryl (HMG)-CoA synthase (HMGS), acetyl-CoA acetyltransferase (ACAT), and a DUF35 protein-that catalyzes an unusual Friedel-Crafts C-acetylation on a pyrrolidine-2,4-dione scaffold, completing the biosynthesis of the antibiotic reutericyclin A. Cryo-electron microscopy of the S. macacae-derived thiolase complex (SmaATase) reveals a conserved architecture resembling the archaeal HMGS/ACAT/DUF35 complex involved in the mevalonate pathway, yet with key catalytic residues rewired to reprogram substrate specificity. Biochemical characterization, molecular modeling, and evolutionary analysis confirmed that the ancestral activity of HMG-CoA synthesis has been lost, while the complex has been repurposed to mediate Friedel-Crafts C-acylation of small molecule acceptors. These findings reveal a rare example of thiolase complex neofunctionalization, shedding light on an underexplored trajectory in enzyme evolution and offering a template for engineering C-C bond-forming catalysts in synthetic biology.
History
DepositionJun 4, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal domain protein
B: 3-oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal domain protein
C: 3-oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal domain protein
D: 3-oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal domain protein
H: 2,4-diacetylphloroglucinol biosynthesis protein PhlB family protein
I: 3-oxoacyl-[acyl-carrier-protein (ACP)] synthase III domain protein
J: 3-oxoacyl-[acyl-carrier-protein (ACP)] synthase III domain protein
K: 2,4-diacetylphloroglucinol biosynthesis protein PhlB family protein
L: 2,4-diacetylphloroglucinol biosynthesis protein PhlB family protein
E: 3-oxoacyl-[acyl-carrier-protein (ACP)] synthase III domain protein
F: 3-oxoacyl-[acyl-carrier-protein (ACP)] synthase III domain protein
G: 2,4-diacetylphloroglucinol biosynthesis protein PhlB family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,00216
Polymers405,74012
Non-polymers2624
Water00
1


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

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Components

#1: Protein
3-oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal domain protein


Mass: 39905.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus macacae NCTC 11558 (bacteria)
Gene: STRMA_1492 / Production host: Escherichia coli (E. coli) / References: UniProt: G5JW78
#2: Protein
2,4-diacetylphloroglucinol biosynthesis protein PhlB family protein


Mass: 16954.482 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus macacae NCTC 11558 (bacteria)
Gene: STRMA_1490 / Production host: Escherichia coli (E. coli) / References: UniProt: G5JW76
#3: Protein
3-oxoacyl-[acyl-carrier-protein (ACP)] synthase III domain protein


Mass: 44574.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus macacae NCTC 11558 (bacteria)
Gene: STRMA_1491 / Production host: Escherichia coli (E. coli) / References: UniProt: G5JW77
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / 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: The multi-component acyltransferase complex MucABC from Streptococcus macacae at a stoichiometric ratio of 4:4:4
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Streptococcus macacae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.18.2_3874model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71520 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00627464
ELECTRON MICROSCOPYf_angle_d0.60337006
ELECTRON MICROSCOPYf_dihedral_angle_d7.523758
ELECTRON MICROSCOPYf_chiral_restr0.0484108
ELECTRON MICROSCOPYf_plane_restr0.0044761

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