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- EMDB-62561: CryoEM structure of a 2,3-hydroxycinnamic acid 1,2-dioxygenase Mh... -

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Basic information

Entry
Database: EMDB / ID: EMD-62561
TitleCryoEM structure of a 2,3-hydroxycinnamic acid 1,2-dioxygenase MhpB in substrate bound form
Map data
Sample
  • Complex: The decamer complex of MhpB bound with its substrate
    • Protein or peptide: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
  • Ligand: FE (II) ION
  • Ligand: 3-[2,3-bis(oxidanyl)phenyl]propanoic acid
Keywords2 / 3-hydroxycinnamic acid 1 / 2-dioxygenase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


phenylpropanoid catabolic process / 3-carboxyethylcatechol 2,3-dioxygenase / 3-carboxyethylcatechol 2,3-dioxygenase activity / 3-(3-hydroxy)phenylpropionate catabolic process / 3-phenylpropionate catabolic process / ferrous iron binding
Similarity search - Function
2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase
Similarity search - Domain/homology
2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsDong X / Jiang WX / Ma LX / Xing Q
Funding support China, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32371277 China
National Science Foundation (NSF, China)32301028 China
CitationJournal: J Hazard Mater / Year: 2025
Title: Structural and catalytic insights into MhpB: A dioxygenase enzyme for degrading catecholic pollutants.
Authors: Xu Dong / Manli Xu / Miao Wu / Ying Wang / Xiaoqi Cheng / Wenxue Jiang / Dule Zheng / Ahmed Habiba Omar / Yibin Cheng / Aitao Li / Lixin Ma / Qiong Xing /
Abstract: The increasing environmental pollution from persistent aromatic compounds requires effective biodegradation strategies. In this study, we focused on MhpB, an extradiol dioxygenase (EDO) from ...The increasing environmental pollution from persistent aromatic compounds requires effective biodegradation strategies. In this study, we focused on MhpB, an extradiol dioxygenase (EDO) from Escherichia coli. It is known for its role in the degradation of catechols, key intermediates in the degradation of aromatic compounds. We report the high-resolution structure of MhpB determined by cryo-electron microscopy, revealing a decameric conformation with the catalytic chamber at the side. The structure-based analysis allowed us to investigate the substrate-enzyme interaction and the substrate selectivity, which are crucial for its catalytic function. Site-directed mutagenesis was used to modulate the in vitro and in vivo substrate preference of MhpB, enhancing its potential for industrial applications in pollutant degradation. The study provides insight into the mechanism of the enzyme and paves the way for the development of engineered EDOs for environmental remediation of aromatic pollutants.
History
DepositionDec 2, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62561.png

Downloads & links

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Map

FileDownload / File: emd_62561.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 400 pix.
= 226.668 Å		0.57 Å/pix.
x 400 pix.
= 226.668 Å		0.57 Å/pix.
x 400 pix.
= 226.668 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.56667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0434
Minimum - Maximum-0.2762499 - 0.53678477
Average (Standard dev.)0.00021936424 (±0.022992404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 226.668 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62561_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62561_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The decamer complex of MhpB bound with its substrate

EntireName: The decamer complex of MhpB bound with its substrate
Components
  • Complex: The decamer complex of MhpB bound with its substrate
    • Protein or peptide: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
  • Ligand: FE (II) ION
  • Ligand: 3-[2,3-bis(oxidanyl)phenyl]propanoic acid

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Supramolecule #1: The decamer complex of MhpB bound with its substrate

SupramoleculeName: The decamer complex of MhpB bound with its substrate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-diox...

MacromoleculeName: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: 3-carboxyethylcatechol 2,3-dioxygenase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 34.230961 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MHAYLHCLSH SPLVGYVDPA QEVLDEVNGV IASARERIAA FSPELVVLFA PDHYNGFFYD VMPPFCLGVG ATAIGDFGSA AGELPVPVE LAEACAHAVM KSGIDLAVSY CMQVDHGFAQ PLEFLLGGLD KVPVLPVFIN GVATPLPGFQ RTRMLGEAIG R FTSTLNKR ...String:
MHAYLHCLSH SPLVGYVDPA QEVLDEVNGV IASARERIAA FSPELVVLFA PDHYNGFFYD VMPPFCLGVG ATAIGDFGSA AGELPVPVE LAEACAHAVM KSGIDLAVSY CMQVDHGFAQ PLEFLLGGLD KVPVLPVFIN GVATPLPGFQ RTRMLGEAIG R FTSTLNKR VLFLGSGGLS HQPPVPELAK ADAHMRDRLL GSGKDLPASE RELRQQRVIS AAEKFVEDQR TLHPLNPIWD NQ FMTLLEQ GRIQELDAVS NEELSAIAGK STHEIKTWVA AFAAISAFGN WRSEGRYYRP IPEWIAGFGS LSARTEN

UniProtKB: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase

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Macromolecule #2: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 2 / Number of copies: 10 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #3: 3-[2,3-bis(oxidanyl)phenyl]propanoic acid

MacromoleculeName: 3-[2,3-bis(oxidanyl)phenyl]propanoic acid / type: ligand / ID: 3 / Number of copies: 10 / Formula: A1EG2
Molecular weightTheoretical: 182.173 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 182651
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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