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- EMDB-19568: DtpB hexamer from Streptomyces lividans -

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Basic information

Entry
Database: EMDB / ID: EMD-19568
TitleDtpB hexamer from Streptomyces lividans
Map data
Sample
  • Complex: Hexamer complex of Dye-type peroxidase B from Streptomyces Lividans
    • Protein or peptide: Dyp-type peroxidase family
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
KeywordsHeme / iron / dye-type peroxidase / METAL BINDING PROTEIN / OXIDOREDUCTASE
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
: / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
Dyp-type peroxidase family
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsWorrall JAR / Chaplin AK / Allport T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci / Year: 2024
Title: The oligomeric states of dye-decolorizing peroxidases from Streptomyces lividans and their implications for mechanism of substrate oxidation.
Authors: Marina Lučić / Thomas Allport / Thomas A Clarke / Lewis J Williams / Michael T Wilson / Amanda K Chaplin / Jonathan A R Worrall /
Abstract: A common evolutionary mechanism in biology to drive function is protein oligomerization. In prokaryotes, the symmetrical assembly of repeating protein units to form homomers is widespread, yet ...A common evolutionary mechanism in biology to drive function is protein oligomerization. In prokaryotes, the symmetrical assembly of repeating protein units to form homomers is widespread, yet consideration in vitro of whether such assemblies have functional or mechanistic consequences is often overlooked. Dye-decolorizing peroxidases (DyPs) are one such example, where their dimeric α + β barrel units can form various oligomeric states, but the oligomer influence, if any, on mechanism and function has received little attention. In this work, we have explored the oligomeric state of three DyPs found in Streptomyces lividans, each with very different mechanistic behaviors in their reactions with hydrogen peroxide and organic substrates. Using analytical ultracentrifugation, we reveal that except for one of the A-type DyPs where only a single sedimenting species is detected, oligomer states ranging from homodimers to dodecamers are prevalent in solution. Using cryo-EM on preparations of the B-type DyP, we determined a 3.02 Å resolution structure of a hexamer assembly that corresponds to the dominant oligomeric state in solution as determined by analytical ultracentrifugation. Furthermore, cryo-EM data detected sub-populations of higher-order oligomers, with one of these formed by an arrangement of two B-type DyP hexamers to give a dodecamer assembly. Our solution and structural insights of these oligomer states provide a new framework to consider previous mechanistic studies of these DyP members and are discussed in terms of long-range electron transfer for substrate oxidation and in the "storage" of oxidizable equivalents on the heme until a two-electron donor is available.
History
DepositionFeb 5, 2024-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19568.png

Downloads & links

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Map

FileDownload / File: emd_19568.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 520 pix.
= 339.04 Å		0.65 Å/pix.
x 520 pix.
= 339.04 Å		0.65 Å/pix.
x 520 pix.
= 339.04 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.652 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0656
Minimum - Maximum-0.07823597 - 0.25963172
Average (Standard dev.)0.00012681875 (±0.006994632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 339.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19568_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_19568_half_map_2.map
Projections & Slices
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Sample components

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Entire : Hexamer complex of Dye-type peroxidase B from Streptomyces Lividans

EntireName: Hexamer complex of Dye-type peroxidase B from Streptomyces Lividans
Components
  • Complex: Hexamer complex of Dye-type peroxidase B from Streptomyces Lividans
    • Protein or peptide: Dyp-type peroxidase family
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: Hexamer complex of Dye-type peroxidase B from Streptomyces Lividans

SupramoleculeName: Hexamer complex of Dye-type peroxidase B from Streptomyces Lividans
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Streptomyces lividans (bacteria)

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Macromolecule #1: Dyp-type peroxidase family

MacromoleculeName: Dyp-type peroxidase family / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces lividans (bacteria)
Molecular weightTheoretical: 34.172223 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGGEVEEPEP QMVLSPLTSA AIFLVVTIDS GGEDTVRDLL SDVASLERAV GFRAQPDGRL SCVTGIGSEA WDRLFSGARP AGLHPFREL DGPVHRAVAT PGDLLFHIRA SRLDLCFALA TEIMGRLRGA VTPQDEVHGF KYFDERDMLG FVDGTENPTG A AARRAVLV ...String:
MGGEVEEPEP QMVLSPLTSA AIFLVVTIDS GGEDTVRDLL SDVASLERAV GFRAQPDGRL SCVTGIGSEA WDRLFSGARP AGLHPFREL DGPVHRAVAT PGDLLFHIRA SRLDLCFALA TEIMGRLRGA VTPQDEVHGF KYFDERDMLG FVDGTENPTG A AARRAVLV GAEDPAFAGG SYAVVQKYLH DIDAWEGLSV EAQERVIGRR KMTDVELSDD VKPADSHVAL TSVTGPDGSD LE ILRDNMP FGSVGREEFG TYFIGYARTP EVTETMLERM FLGTASAPHD RILDFSTAVT GSLFFTPAAD FLEDLSARP

UniProtKB: Dyp-type peroxidase family

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 6 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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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
GridMaterial: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 47.19 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6yr4

Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 24402
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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