[English] 日本語
Yorodumi
- EMDB-42114: Cryo-EM structure of the AlbAB cyclodipeptide oxidase enzyme filament -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42114
TitleCryo-EM structure of the AlbAB cyclodipeptide oxidase enzyme filament
Map datastructure of the AlbAB cyclodipeptide oxidase enzyme filament
Sample
  • Complex: AlbAB cyclodipeptide oxidase enzyme filament
    • Protein or peptide: Albonoursin synthase
    • Protein or peptide: Protein AlbB
  • Ligand: FLAVIN MONONUCLEOTIDE
Keywordscyclodipeptide oxidase / cyclic dipeptide oxidase / nitroreductase-like / enzyme filament / flavoenzyme / OXIDOREDUCTASE
Function / homology
Function and homology information


albonoursin synthase / oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor / cytoplasm
Similarity search - Function
Protein of unknown function DUF6092 / Family of unknown function (DUF6092) / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
Protein AlbB / Albonoursin synthase
Similarity search - Component
Biological speciesStreptomyces noursei ATCC 11455 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsAndreas MP / Giessen TW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133325 United States
CitationJournal: Nat Commun / Year: 2024
Title: Cyclodipeptide oxidase is an enzyme filament.
Authors: Michael P Andreas / Tobias W Giessen /
Abstract: Modified cyclic dipeptides represent a widespread class of secondary metabolites with diverse pharmacological activities, including antibacterial, antifungal, and antitumor. Here, we report the ...Modified cyclic dipeptides represent a widespread class of secondary metabolites with diverse pharmacological activities, including antibacterial, antifungal, and antitumor. Here, we report the structural characterization of the Streptomyces noursei enzyme AlbAB, a cyclodipeptide oxidase (CDO) carrying out α,β-dehydrogenations during the biosynthesis of the antibiotic albonoursin. We show that AlbAB is a megadalton heterooligomeric enzyme filament containing covalently bound flavin mononucleotide cofactors. We highlight that AlbAB filaments consist of alternating dimers of AlbA and AlbB and that enzyme activity is crucially dependent on filament formation. We show that AlbA-AlbB interactions are highly conserved suggesting that other CDO-like enzymes are likely enzyme filaments. As CDOs have been employed in the structural diversification of cyclic dipeptides, our results will be useful for future applications of CDOs in biocatalysis and chemoenzymatic synthesis.
History
DepositionSep 25, 2023-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42114.png

Downloads & links

-
Map

FileDownload / File: emd_42114.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of the AlbAB cyclodipeptide oxidase enzyme filament
Voxel sizeX=Y=Z: 0.8487 Å
Density
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.6960582 - 2.3135126
Average (Standard dev.)-0.000016420823 (±0.038507942)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 305.53198 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map 1

Fileemd_42114_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map 2

Fileemd_42114_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : AlbAB cyclodipeptide oxidase enzyme filament

EntireName: AlbAB cyclodipeptide oxidase enzyme filament
Components
  • Complex: AlbAB cyclodipeptide oxidase enzyme filament
    • Protein or peptide: Albonoursin synthase
    • Protein or peptide: Protein AlbB
  • Ligand: FLAVIN MONONUCLEOTIDE

-
Supramolecule #1: AlbAB cyclodipeptide oxidase enzyme filament

SupramoleculeName: AlbAB cyclodipeptide oxidase enzyme filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Streptomyces noursei ATCC 11455 (bacteria)

-
Macromolecule #1: Albonoursin synthase

MacromoleculeName: Albonoursin synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces noursei ATCC 11455 (bacteria)
Molecular weightTheoretical: 21.071307 KDa
Recombinant expressionOrganism: Streptomyces coelicolor A3(2) (bacteria)
SequenceString: MLAHSSSESP PESLPDAWTV LKTRTAVRNY AKEPVDDALI EQLLEAMLAA PTASNRQAWS FMVVRRPAAV RRLRAFSPGV LGTPAFFVV ACVDRSLTDN LSPKLSQKIY DTSKLCVAMA VENLLLAAHA AGLGGCPVGS FRSDIVTSML GIPEHIEPML V VPIGRPAT ...String:
MLAHSSSESP PESLPDAWTV LKTRTAVRNY AKEPVDDALI EQLLEAMLAA PTASNRQAWS FMVVRRPAAV RRLRAFSPGV LGTPAFFVV ACVDRSLTDN LSPKLSQKIY DTSKLCVAMA VENLLLAAHA AGLGGCPVGS FRSDIVTSML GIPEHIEPML V VPIGRPAT ALVPSQRRAK NEVVNYESWG NRAAAPTA

UniProtKB: Albonoursin synthase

-
Macromolecule #2: Protein AlbB

MacromoleculeName: Protein AlbB / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces noursei ATCC 11455 (bacteria)
Molecular weightTheoretical: 11.583143 KDa
Recombinant expressionOrganism: Streptomyces coelicolor A3(2) (bacteria)
SequenceString:
MNPGETVLPP QLREEIALLA VYLLSSGRGL LEEPADYGIY RCTDGARRAL QLLDEHGGST ARLTAVRERL DEVMFAPMGE DRDMGAILD DLCRQMADAL PEIETP

UniProtKB: Protein AlbB

-
Macromolecule #3: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 2 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.75 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
20.0 mMC4H11NO3Tris

Details: 20 mM NaCl, 150 mM Tris pH 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
Details: Grid was glow discharged for 60 seconds at 5 mA under vacuum
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Details: Grid was plunge frozen into liquid ethane using the following parameters: blot force- 5, blot time 2 seconds.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 1 / Number real images: 3015 / Average exposure time: 2.03063 sec. / Average electron dose: 50.12 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Segment selectionNumber selected: 1202923 / Software - Name: cryoSPARC (ver. 4.2.1)
Startup modelType of model: INSILICO MODEL
In silico model: An initial map was created using CryoSPARC HelixRefine on selected filament particles
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 46.063 Å
Applied symmetry - Helical parameters - Δ&Phi: 119.969 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1)
Details: Final reconstruction was generated by a masked local refinement of the helically refined map. The mask encompassed one dimer of AlbA and two surrounding dimers of AlbB.
Number images used: 795765
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsA model of AlbAB was created using AlphaFold2 using MMseqs2 via ColabFold. The model was then fit into the cryoEM density using ChimeraX. The model was then iteratively refined using Coot v 0.9.8.1 and real-space refinement in Phenix v 1.20.1-4487.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 107.4 / Target criteria: Cross-correlation coefficient
Output model

PDB-8uc3:
Cryo-EM structure of the AlbAB cyclodipeptide oxidase enzyme filament

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more