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- EMDB-61388: Structure of chanoclavine synthase from Claviceps fusiformis in c... -

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Basic information

Entry
Database: EMDB / ID: EMD-61388
TitleStructure of chanoclavine synthase from Claviceps fusiformis in complex with prechanoclavine
Map data
Sample
  • Complex: Ergot alkaloid synthesis protein C
    • Protein or peptide: Catalase easC
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (2~{S})-2-(methylamino)-3-[4-[(1~{E})-3-methylbuta-1,3-dienyl]-1~{H}-indol-3-yl]propanoic acid
KeywordsAlkaloid metabolism / Metal-binding / Heme / Oxidoreductase / Peroxidase
Function / homology
Function and homology information


Oxidoreductases; Acting on a peroxide as acceptor / indole alkaloid biosynthetic process / catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily
Similarity search - Domain/homology
Biological speciesClaviceps fusiformis (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.33 Å
AuthorsLiu ZW / Wang T / Li X / Shen PP / Huang J-W / Chen C-C / Guo R-T
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2025
Title: Chanoclavine synthase operates by an NADPH-independent superoxide mechanism.
Authors: Chun-Chi Chen / Zhi-Pu Yu / Ziwei Liu / Yongpeng Yao / Peter-Leon Hagedoorn / Rob Alexander Schmitz / Lujia Yang / Lu Yu / Aokun Liu / Xiang Sheng / Hao Su / Yaqing Ma / Te Wang / Jian-Wen ...Authors: Chun-Chi Chen / Zhi-Pu Yu / Ziwei Liu / Yongpeng Yao / Peter-Leon Hagedoorn / Rob Alexander Schmitz / Lujia Yang / Lu Yu / Aokun Liu / Xiang Sheng / Hao Su / Yaqing Ma / Te Wang / Jian-Wen Huang / Lilan Zhang / Juzhang Yan / Jinping Bao / Chengsen Cui / Xian Li / Panpan Shen / Wuyuan Zhang / Jian Min / Chang-Yun Wang / Rey-Ting Guo / Shu-Shan Gao /
Abstract: More than ten ergot alkaloids comprising both natural and semi-synthetic products are used to treat various diseases. The central C ring forms the core pharmacophore for ergot alkaloids, giving them ...More than ten ergot alkaloids comprising both natural and semi-synthetic products are used to treat various diseases. The central C ring forms the core pharmacophore for ergot alkaloids, giving them structural similarity to neurotransmitters, thus enabling their modulation of neurotransmitter receptors. The haem catalase chanoclavine synthase (EasC) catalyses the construction of this ring through complex radical oxidative cyclization. Unlike canonical catalases, which catalyse HO disproportionation, EasC and its homologues represent a broader class of catalases that catalyse O-dependent radical reactions. We have elucidated the structure of EasC by cryo-electron microscopy, revealing a nicotinamide adenine dinucleotide phosphate (reduced) (NADPH)-binding pocket and a haem pocket common to all haem catalases, with a unique homodimeric architecture that is, to our knowledge, previously unobserved. The substrate prechanoclavine unprecedentedly binds in the NADPH-binding pocket, instead of the previously suspected haem-binding pocket, and two pockets were connected by a slender tunnel. Contrary to the established mechanisms, EasC uses superoxide rather than the more generally used transient haem iron-oxygen complexes (such as compounds I, II and III), to mediate substrate transformation through superoxide-mediated cooperative catalysis of the two distant pockets. We propose that this reactive oxygen species mechanism could be widespread in metalloenzyme-catalysed reactions.
History
DepositionAug 31, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61388.png

Downloads & links

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Map

FileDownload / File: emd_61388.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.34
Minimum - Maximum-1.4739196 - 2.7584488
Average (Standard dev.)-0.000107668166 (±0.067101985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61388_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61388_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Ergot alkaloid synthesis protein C

EntireName: Ergot alkaloid synthesis protein C
Components
  • Complex: Ergot alkaloid synthesis protein C
    • Protein or peptide: Catalase easC
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (2~{S})-2-(methylamino)-3-[4-[(1~{E})-3-methylbuta-1,3-dienyl]-1~{H}-indol-3-yl]propanoic acid

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Supramolecule #1: Ergot alkaloid synthesis protein C

SupramoleculeName: Ergot alkaloid synthesis protein C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Claviceps fusiformis (fungus)

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Macromolecule #1: Catalase easC

MacromoleculeName: Catalase easC / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on a peroxide as acceptor
Source (natural)Organism: Claviceps fusiformis (fungus)
Molecular weightTheoretical: 54.045656 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASQVSLTAQ GSGLSAPLNG PEHLTSTTVE NDPRLLDILS RFNREKIPER AVHARGAGAY GEFEVTHDVS DICDIDMLLG IGKKTPCAV RFSTTALERG SAESVRDVKG MAIKLFTGDG EWDWVCLNIP MFFIRDPSKF PDLVHAQRPD PATNLANPAA W WEFVCNNH ...String:
MASQVSLTAQ GSGLSAPLNG PEHLTSTTVE NDPRLLDILS RFNREKIPER AVHARGAGAY GEFEVTHDVS DICDIDMLLG IGKKTPCAV RFSTTALERG SAESVRDVKG MAIKLFTGDG EWDWVCLNIP MFFIRDPSKF PDLVHAQRPD PATNLANPAA W WEFVCNNH ESLHMAVFLF TDFGTMFDYR SMSGYVSHAY KWVMPDGTWK YVHWFLASDQ GPNFEQGNQT REAAPNDSES AT RDLYQSL ERGECPSWTV KVQVIDPEDA PRLAFNILDV SKHWNLGNYP PDIPVIPERC VGKLTLKKGP ENYFEEIEKL AFS PSHLVH GVEPSEDPML QARLFAYPDA QEHRLGPQFS DMAAKRTGHA ANDAPKTKKP AVPLQKQSRE HAEWVSQVTS SSWS QPNET DYKFPRELWA ALPRLRGEEF QNRLVVNMAE SVSQIPEDLR QKVYKTLALV AEDLASRVES LTEEMVVPEQ RPRL

UniProtKB: Catalase easC

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #3: (2~{S})-2-(methylamino)-3-[4-[(1~{E})-3-methylbuta-1,3-dienyl]-1~...

MacromoleculeName: (2~{S})-2-(methylamino)-3-[4-[(1~{E})-3-methylbuta-1,3-dienyl]-1~{H}-indol-3-yl]propanoic acid
type: ligand / ID: 3 / Number of copies: 2 / Formula: LH6
Molecular weightTheoretical: 284.353 Da

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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: 7.5 / Details: 20 mM Tris-HCL, 150 mM NaCl,pH 7.5
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: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 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: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 115524
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9jdc:
Structure of chanoclavine synthase from Claviceps fusiformis in complex with prechanoclavine

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