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- EMDB-26344: YcaO-mediated ATP-dependent peptidase activity in ribosomal pepti... -

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Basic information

Entry
Database: EMDB / ID: EMD-26344
TitleYcaO-mediated ATP-dependent peptidase activity in ribosomal peptide biosynthesis
Map data
Sample
  • Complex: MusD
    • Protein or peptide: MusD
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
Function / homologyBacteriocin biosynthesis, cyclodehydratase domain / Thiazole/oxazole-forming peptide maturase, SagD family component / YcaO-like domain / YcaO cyclodehydratase, ATP-ad Mg2+-binding / YcaO domain profile. / ubiquitin-like modifier activating enzyme activity / Ubiquitin-activating enzyme / MusD
Function and homology information
Biological speciesDesmonostoc sp. PCC 7906 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZheng Y / Nair SK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM079038 United States
CitationJournal: Nat Chem Biol / Year: 2023
Title: YcaO-mediated ATP-dependent peptidase activity in ribosomal peptide biosynthesis.
Authors: Yiwu Zheng / Satish K Nair /
Abstract: YcaO enzymes catalyze ATP-dependent post-translation modifications on peptides, including the installation of (ox/thi)azoline, thioamide and/or amidine moieties. Here we demonstrate that, in the ...YcaO enzymes catalyze ATP-dependent post-translation modifications on peptides, including the installation of (ox/thi)azoline, thioamide and/or amidine moieties. Here we demonstrate that, in the biosynthesis of the bis-methyloxazolic alkaloid muscoride A, the YcaO enzyme MusD carries out both ATP-dependent cyclodehydration and peptide bond cleavage, which is a mechanism unprecedented for such a reaction. YcaO-catalyzed modifications are proposed to occur through a backbone O-phosphorylated intermediate, but this mechanism remains speculative. We report, to our knowedge, the first characterization of an acyl-phosphate species consistent with the proposed mechanism for backbone amide activation. The 3.1-Å-resolution cryogenic electron microscopy structure of MusD along with biochemical analysis allow identification of residues that enable peptide cleavage reaction. Bioinformatics analysis identifies other cyanobactin pathways that may deploy bifunctional YcaO enzymes. Our structural, mutational and mechanistic studies expand the scope of modifications catalyzed by YcaO proteins to include peptide hydrolysis and provide evidence for a unifying mechanism for the catalytically diverse outcomes.
History
DepositionMar 1, 2022-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateJan 11, 2023-
Current statusJan 11, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26344.png

Downloads & links

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Map

FileDownload / File: emd_26344.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 337.28 Å		1.05 Å/pix.
x 320 pix.
= 337.28 Å		1.05 Å/pix.
x 320 pix.
= 337.28 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.1926337 - 2.479223
Average (Standard dev.)-0.0014885309 (±0.041723765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 337.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26344_msk_1.map
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Half map: #1

Fileemd_26344_half_map_1.map
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Half map: #2

Fileemd_26344_half_map_2.map
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Sample components

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Entire : MusD

EntireName: MusD
Components
  • Complex: MusD
    • Protein or peptide: MusD
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: MusD

SupramoleculeName: MusD / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Desmonostoc sp. PCC 7906 (bacteria)
Molecular weightTheoretical: 88.76 kDa/nm

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Macromolecule #1: MusD

MacromoleculeName: MusD / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Desmonostoc sp. PCC 7906 (bacteria) / Strain: PCC 7906
Molecular weightTheoretical: 88.844805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMKILQIK PHFRAEIIEP KHVYLLSESS THALTGELYC QLIPLLNGNY TVDEIINKLQ VDPSHIDYAL ERLQARGYIT EAIPQLTPE AVAFWGLLKV EPQVAYQCLQ QTQVYVSSVV NLPTQPLITA LEEVGIKAIN WDGELQEFPP HSLLVVLTDD Y LQPQLNKI ...String:
SNAMKILQIK PHFRAEIIEP KHVYLLSESS THALTGELYC QLIPLLNGNY TVDEIINKLQ VDPSHIDYAL ERLQARGYIT EAIPQLTPE AVAFWGLLKV EPQVAYQCLQ QTQVYVSSVV NLPTQPLITA LEEVGIKAIN WDGELQEFPP HSLLVVLTDD Y LQPQLNKI NQIALKANQP WLLIKPVGTI LWLGPIFQPQ ITGCWECLAQ RLRVNREVEA SVLRQKNSSL QLSPSQELNS SV LQSNGNG VKSEVIECLP PPAAVIPSTL QTALHLATTE IAKWIVKQGV EDTTPFPTLE GKVITFDQRN LDLQTHILSL RPQ CPSCGN PNLLTERAFQ PLVLSSRKKQ FTSDGGHRAF SPDQTVNRYQ HLISPITGVV TSLVRASDPN DSLNHTYNAV HSFV IASNI GRMRRYLKHK SSGKGKTDSQ SKASGFCEAI ERYSGVYQGD EPRISATLAE LGEKAIHPAR CSLFSSEQYE YREEF NRRG GVFDWIPQPF DETKVIEWTP VWSLTEQTHK YIPTAYCYYG YPLPEDHEFC RANSNGDATG NTLEEAIIQG FFEIVE RDS VAIWWYNRLK RPAVDLASFN EPYLLEVQDL YRSNNRDLWV IDITADLDIP TFVAVSYLKD NKHQTILLGF GTHFDPK IA ILRAVTEVNQ IAFTCDGVEV TKEFVEMREW FKKATIENQP YLVPDSTVPA KVYQDYQQRW SDDIYEDVMT CVEISKNA G LETLVLDKTR PDIGLNVAKV IVPEMPHYWL RMGAKRIYDV PVKMGWLSTP LTEEQMNPIS VPI

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration6 mg/mL
BufferpH: 7.5 / Details: HEPES pH 7.5. 25 mM KCl.
GridMaterial: COPPER
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.33 e/Å2

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 123786
FSC plot (resolution estimation)

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