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- EMDB-32864: Structure of an assembly-line polyketide synthase module with typ... -

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Entry
Database: EMDB / ID: EMD-32864
TitleStructure of an assembly-line polyketide synthase module with typical docking domain position
Map data
Sample
  • Organelle or cellular component: an assembly-line polyketide synthase module containing KS-AT-DH-KR domains
Keywordsmegaenzyme / HYDROLASE
Biological speciesStreptomyces chartreusis NRRL 3882cha (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.55 Å
AuthorsWang J / Wang Z
Funding support China, 1 items
OrganizationGrant numberCountry
Other government2019YFA0905400 China
CitationJournal: Nat Commun / Year: 2023
Title: C-N bond formation by a polyketide synthase.
Authors: Jialiang Wang / Xiaojie Wang / Xixi Li / LiangLiang Kong / Zeqian Du / Dandan Li / Lixia Gou / Hao Wu / Wei Cao / Xiaozheng Wang / Shuangjun Lin / Ting Shi / Zixin Deng / Zhijun Wang / Jingdan Liang /
Abstract: Assembly-line polyketide synthases (PKSs) are molecular factories that produce diverse metabolites with wide-ranging biological activities. PKSs usually work by constructing and modifying the ...Assembly-line polyketide synthases (PKSs) are molecular factories that produce diverse metabolites with wide-ranging biological activities. PKSs usually work by constructing and modifying the polyketide backbone successively. Here, we present the cryo-EM structure of CalA3, a chain release PKS module without an ACP domain, and its structures with amidation or hydrolysis products. The domain organization reveals a unique "∞"-shaped dimeric architecture with five connected domains. The catalytic region tightly contacts the structural region, resulting in two stabilized chambers with nearly perfect symmetry while the N-terminal docking domain is flexible. The structures of the ketosynthase (KS) domain illustrate how the conserved key residues that canonically catalyze C-C bond formation can be tweaked to mediate C-N bond formation, revealing the engineering adaptability of assembly-line polyketide synthases for the production of novel pharmaceutical agents.
History
DepositionFeb 12, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateOct 11, 2023-
Current statusOct 11, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32864.png

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Map

FileDownload / File: emd_32864.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.023766464 - 0.05125681
Average (Standard dev.)0.00019335547 (±0.003125431)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_32864_additional_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_32864_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_32864_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : an assembly-line polyketide synthase module containing KS-AT-DH-K...

EntireName: an assembly-line polyketide synthase module containing KS-AT-DH-KR domains
Components
  • Organelle or cellular component: an assembly-line polyketide synthase module containing KS-AT-DH-KR domains

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Supramolecule #1: an assembly-line polyketide synthase module containing KS-AT-DH-K...

SupramoleculeName: an assembly-line polyketide synthase module containing KS-AT-DH-KR domains
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Streptomyces chartreusis NRRL 3882cha (bacteria)
Molecular weightTheoretical: 0.36 kDa/nm

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36984
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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