[English] 日本語
Yorodumi
- PDB-8k04: CryoEM structure of a 2,3-hydroxycinnamic acid 1,2-dioxygenase Mh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8k04
TitleCryoEM structure of a 2,3-hydroxycinnamic acid 1,2-dioxygenase MhpB in apo form
Components2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
KeywordsBIOSYNTHETIC PROTEIN / dioxygenase
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsJiang, W.X. / Cheng, X.Q. / Ma, L.X. / Xing, Q.
Funding support China, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
B: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
C: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
D: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
E: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
F: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
G: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
H: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
I: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
J: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase


Theoretical massNumber of molelcules
Total (without water)342,31010
Polymers342,31010
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "I"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "A"
d_9ens_1chain "H"
d_10ens_1chain "J"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 1 - 314 / Label seq-ID: 1 - 314

Dom-IDAuth asym-IDLabel asym-ID
d_1II
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF
d_7GG
d_8AA
d_9HH
d_10JJ

NCS oper:
IDCodeMatrixVector
1given(0.808508235774, 0.588484708174, -0.000425359806766), (0.588484709384, -0.80850833542, -0.00013556219422), (-0.000423683227628, -0.000140714591782, -0.999999900346)-44.9542060212, 138.286012163, 225.608520029
2given(-0.307644442918, 0.951498548391, -0.00232575820088), (0.951500687407, 0.307646268614, 0.000463973656586), (0.00115698109293, -0.00207022160977, -0.999997187785)40.6997977644, -29.4378870861, 225.530092875
3given(-0.999999632509, -0.000857310542655, 5.13535288825E-7), (-0.000857310602994, 0.99999962379, -0.000132053879671), (-4.00323912387E-7, -0.000132054271402, -0.999999991281)226.750411017, 0.117807479847, 225.559790304
4given(-0.308929199831, -0.951084969515, -0.00036090768756), (-0.951084540193, 0.308929404142, -0.000905904303087), (0.000973086963353, 6.33934305994E-5, -0.999999524541)256.165010141, 186.247272719, 225.442740911
5given(-0.809004426024, 0.58780245047, 0.000343357453974), (-0.587802399697, -0.809004498878, 0.00024434904909), (0.000421406694813, -4.14687319108E-6, 0.9999999112)138.354444135, 271.608740465, -0.0472606961796
6given(-0.808972917699, -0.587845735804, 0.000457522536619), (0.587845813492, -0.808972989356, 4.52978482369E-5), (0.000343495227219, 0.000305597440184, 0.999999894311)271.572312901, 138.385310804, -0.0706498811306
7given(0.807121441518, -0.5903829212, 0.00172771431039), (-0.590381938567, -0.807123278012, -0.0010866023769), (0.00203598992313, -0.000142991247053, -0.999997917147)88.4628623179, 271.840926066, 225.327728411
8given(0.308974740648, -0.951070221461, 0.000208547924418), (0.9510702407, 0.308974712894, -0.000155071162904), (8.30475301732E-5, 0.000246256797014, 0.99999996623)186.072085514, -29.4462198005, -0.0373251156164
9given(0.309067049499, 0.951040247743, 7.80225454768E-5), (-0.951040227373, 0.309067022534, 0.000247992105085), (0.000211736277237, -0.000150848767608, 0.999999966206)-29.4980237987, 186.059069001, -0.0067230314217

-
Components

#1: Protein
2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase / 3-carboxyethylcatechol 2 / 3-dioxygenase


Mass: 34230.961 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: mhpB, mhpB_1, A6592_08360, AAG43_003122, ACU57_18785, AM464_18695, AT845_003692, AW119_11075, BEA19_09385, BF481_002201, BG944_000993, BGM66_001457, BJI68_13680, BJJ90_20525, BKL28_002951, ...Gene: mhpB, mhpB_1, A6592_08360, AAG43_003122, ACU57_18785, AM464_18695, AT845_003692, AW119_11075, BEA19_09385, BF481_002201, BG944_000993, BGM66_001457, BJI68_13680, BJJ90_20525, BKL28_002951, BLM69_004076, BMC79_001945, BMT50_03125, BMT91_19310, BON92_03390, BTB68_001828, BUO55_000492, BvCmsKKP061_02674, BXT93_09690, BZL69_13825, C0P57_002705, C2R31_002140, C3F40_10810, C5N07_24670, C9E67_23975, CA593_01390, CDL36_14360, CDL37_09265, CG831_000406, CIG67_02690, CQ986_000779, CV83915_01226, CX938_004022, D0X26_07210, D4M65_16025, D9H94_11950, DN627_27135, DTL43_07625, DTL90_10525, DTM45_10750, DU321_19275, E4K51_23600, E5H86_16710, E6D34_13465, EA435_05985, EAN77_08135, EAX79_07015, EBP16_14625, ECs0403, EIZ93_16195, EL79_3496, ELT17_10045, ELT48_00575, ELX68_17755, ELX76_06030, ELX79_17290, EPS76_18260, ERS139208_01777, ExPECSC038_04860, F7F11_06665, F9413_17095, F9461_15720, F9S83_01345, FDM60_22665, FJQ53_15090, FKO60_15565, FOI11_011700, FOI11_08345, FPI65_01895, FV293_06300, FVB16_14265, FWK02_24950, FZU14_00995, G3565_02695, G3V95_15725, G4A38_05225, G4A47_03610, GF699_21980, GFY34_04780, GIB53_19760, GJ11_02180, GJO56_07880, GKF66_16190, GKF89_21475, GNW61_15375, GOP25_04445, GP944_04070, GP965_12675, GQM13_16935, GQM21_19370, GRC73_20955, GRW05_10415, GRW57_19650, GSM54_06355, GUI33_03835, H0O72_17150, HEP30_020365, HHH44_001337, HI055_001759, HIE29_000752, HJQ60_002399, HKA49_003062, HLV18_07550, HLX92_10820, HLZ50_17845, HMV95_12485, HV109_18305, HVY77_20140, HVZ29_04840, HX136_19710, IH772_19545, J4S20_003623, J5U05_003482, NCTC10418_05740, NCTC10429_03811, NCTC10764_05415, NCTC10974_04398, NCTC11126_05668, NCTC12950_04217, NCTC13127_05199, NCTC13148_06746, NCTC13216_02859, NCTC8179_01606, NCTC8333_04573, NCTC8450_01327, NCTC8622_02936, NCTC9044_03463, NCTC9045_04477, NCTC9073_03083, NCTC9077_04839, NCTC9111_04016, NCTC9962_02508, ND22_001410, SAMEA3472044_00503, SAMEA3472056_02987, SAMEA3751407_04552, SAMEA3752557_00177, SAMEA3753106_00568, WR15_20705
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C3TMW2, 3-carboxyethylcatechol 2,3-dioxygenase
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Homohexamer of inositol phosphate phosphatase SopB / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 39 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 364814 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 161.15 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.010924740
ELECTRON MICROSCOPYf_angle_d0.742933650
ELECTRON MICROSCOPYf_chiral_restr0.04673680
ELECTRON MICROSCOPYf_plane_restr0.00464460
ELECTRON MICROSCOPYf_dihedral_angle_d5.06223380
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2IIELECTRON MICROSCOPYNCS constraints0.000708921267193
ens_1d_3IIELECTRON MICROSCOPYNCS constraints0.000699238984342
ens_1d_4IIELECTRON MICROSCOPYNCS constraints0.000715794740102
ens_1d_5IIELECTRON MICROSCOPYNCS constraints0.0742115612656
ens_1d_6IIELECTRON MICROSCOPYNCS constraints0.00070869891733
ens_1d_7IIELECTRON MICROSCOPYNCS constraints0.0742149278015
ens_1d_8IIELECTRON MICROSCOPYNCS constraints0.000707948234127
ens_1d_9IIELECTRON MICROSCOPYNCS constraints0.000701542354302
ens_1d_10IIELECTRON MICROSCOPYNCS constraints0.00070690614069

+
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