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- EMDB-36757: CryoEM structure of a 2,3-hydroxycinnamic acid 1,2-dioxygenase Mh... -

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Basic information

Entry
Database: EMDB / ID: EMD-36757
TitleCryoEM structure of a 2,3-hydroxycinnamic acid 1,2-dioxygenase MhpB in apo form
Map data
Sample
  • Complex: Homohexamer of inositol phosphate phosphatase SopB
    • Protein or peptide: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
Keywordsdioxygenase / BIOSYNTHETIC PROTEIN
Function / homology3-carboxyethylcatechol 2,3-dioxygenase / 3-carboxyethylcatechol 2,3-dioxygenase activity / 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 / 3-phenylpropionate catabolic process / ferrous iron binding / 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsJiang WX / Cheng XQ / Ma LX / Xing Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 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
DepositionJul 7, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36757.png

Downloads & links

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Map

FileDownload / File: emd_36757.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.56667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.04420653 - 0.14373596
Average (Standard dev.)0.0002270471 (±0.007908443)
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_36757_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36757_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homohexamer of inositol phosphate phosphatase SopB

EntireName: Homohexamer of inositol phosphate phosphatase SopB
Components
  • Complex: Homohexamer of inositol phosphate phosphatase SopB
    • Protein or peptide: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase

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Supramolecule #1: Homohexamer of inositol phosphate phosphatase SopB

SupramoleculeName: Homohexamer of inositol phosphate phosphatase SopB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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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 (E. coli)
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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
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: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 1.5 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 364814
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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