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- EMDB-60840: Cryo-EM structure of MxaF/MxaJ/PQQ complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60840
TitleCryo-EM structure of MxaF/MxaJ/PQQ complex
Map data
Sample
  • Complex: MxaF/MxaJ/PQQ complex
    • Protein or peptide: Methanol dehydrogenase, alpha subunit
    • Protein or peptide: Methanol oxidation protein MxaJ
  • Ligand: PYRROLOQUINOLINE QUINONE
KeywordsMxaF/MxaJ/PQQ / PROTEIN BINDING
Function / homology
Function and homology information


methanol catabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With a cytochrome as acceptor / oxidoreductase activity, acting on CH-OH group of donors / outer membrane-bounded periplasmic space / periplasmic space / calcium ion binding / membrane
Similarity search - Function
Methanol oxidation system protein MoxJ / Bacterial quinoprotein dehydrogenases signature 1. / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Pyrrolo-quinoline quinone repeat ...Methanol oxidation system protein MoxJ / Bacterial quinoprotein dehydrogenases signature 1. / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Pyrrolo-quinoline quinone repeat / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily
Similarity search - Domain/homology
Methanol dehydrogenase, alpha subunit / Methanol oxidation protein MxaJ
Similarity search - Component
Biological speciesMethylorubrum extorquens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsSun JQ / Gao F
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82272379 China
CitationJournal: Nat Commun / Year: 2025
Title: Deciphering the assembly process of PQQ dependent methanol dehydrogenase.
Authors: Haichuan Zhou / Junqing Sun / Jian Cheng / Min Wu / Jie Bai / Qian Li / Jie Shen / Manman Han / Chen Yang / Liangpo Li / Yuwan Liu / Qichen Cao / Weidong Liu / Haixia Xiao / Hongjun Dong / ...Authors: Haichuan Zhou / Junqing Sun / Jian Cheng / Min Wu / Jie Bai / Qian Li / Jie Shen / Manman Han / Chen Yang / Liangpo Li / Yuwan Liu / Qichen Cao / Weidong Liu / Haixia Xiao / Hongjun Dong / Feng Gao / Huifeng Jiang /
Abstract: Pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenases (MDHs), the periplasmic metalloenzymes in Gram-negative methylotrophic bacteria, play a pivotal role in methane and methanol bio- ...Pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenases (MDHs), the periplasmic metalloenzymes in Gram-negative methylotrophic bacteria, play a pivotal role in methane and methanol bio-utilization. Although the structures of many PQQ-dependent MDHs have been resolved, including the canonical heterotetrameric enzymes composed of two MxaF and two MxaI subunits with a molecule of PQQ and a calcium ion in the active site in MxaF, the biogenesis of these enzymes remains elusive. Here, we characterize a chaperone, MxaJ, responsible for PQQ incorporation by reconstructing a PQQ-dependent MDH assembly system in Escherichia coli. Using cryo-electron microscopy, we capture the structures of the intermediate complexes formed by the chaperone MxaJ and catalytic subunit MxaF during PQQ-dependent MDH maturation, revealing a chaperone-mediated molecular mechanism of cofactor incorporation. These findings not only advance our understanding on the biogenesis of PQQ-dependent MDH, but also provide an alternative engineering way for methane and methanol bioconversion.
History
DepositionJul 18, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60840.png

Downloads & links

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Map

FileDownload / File: emd_60840.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 360 pix.
= 320.4 Å		0.89 Å/pix.
x 360 pix.
= 320.4 Å		0.89 Å/pix.
x 360 pix.
= 320.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.246
Minimum - Maximum-0.55687416 - 1.3177346
Average (Standard dev.)-0.0021293638 (±0.034293503)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 320.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60840_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60840_half_map_2.map
Projections & Slices
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Sample components

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Entire : MxaF/MxaJ/PQQ complex

EntireName: MxaF/MxaJ/PQQ complex
Components
  • Complex: MxaF/MxaJ/PQQ complex
    • Protein or peptide: Methanol dehydrogenase, alpha subunit
    • Protein or peptide: Methanol oxidation protein MxaJ
  • Ligand: PYRROLOQUINOLINE QUINONE

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Supramolecule #1: MxaF/MxaJ/PQQ complex

SupramoleculeName: MxaF/MxaJ/PQQ complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Methylorubrum extorquens (bacteria)

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Macromolecule #1: Methanol dehydrogenase, alpha subunit

MacromoleculeName: Methanol dehydrogenase, alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on the CH-OH group of donors; With a cytochrome as acceptor
Source (natural)Organism: Methylorubrum extorquens (bacteria)
Molecular weightTheoretical: 69.335836 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSRFVTSVSA LAMLALAPAA LSSGAYANDK LVELSKSDDN WVMPGKNYDS NNFSDLKQIN KGNVKQLRPA WTFSTGLLNG HEGAPLVVD GKMYIHTSFP NNTFALGLDD PGTILWQDKP KQNPAARAVA CCDLVNRGLA YWPGDGKTPA LILKTQLDGN V AALNAETG ...String:
MSRFVTSVSA LAMLALAPAA LSSGAYANDK LVELSKSDDN WVMPGKNYDS NNFSDLKQIN KGNVKQLRPA WTFSTGLLNG HEGAPLVVD GKMYIHTSFP NNTFALGLDD PGTILWQDKP KQNPAARAVA CCDLVNRGLA YWPGDGKTPA LILKTQLDGN V AALNAETG ETVWKVENSD IKVGSTLTIA PYVVKDKVII GSSGAELGVR GYLTAYDVKT GEQVWRAYAT GPDKDLLLAS DF NIKNPHY GQKGLGTGTW EGDAWKIGGG TNWGWYAYDP GTNLIYFGTG NPAPWNETMR PGDNKWTMTI FGRDADTGEA KFG YQKTPH DEWDYAGVNV MMLSEQKDKD GKARKLLTHP DRNGIVYTLD RTDGALVSAN KLDDTVNVFK SVDLKTGQPV RDPE YGTRM DHLAKDICPS AMGYHNQGHD SYDPKRELFF MGINHICMDW EPFMLPYRAG QFFVGATLNM YPGPKGDRQN YEGLG QIKA YNAITGDYKW EKMERFAVWG GTMATAGDLV FYGTLDGYLK ARDSDTGDLL WKFKIPSGAI GYPMTYTHKG TQYVAI YYG VGGWPGVGLV FDLADPTAGL GAVGAFKKLA NYTQMGGGVV VFSLDGKGPY DDPNVGEWKS AAKHHHHHH

UniProtKB: Methanol dehydrogenase, alpha subunit

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Macromolecule #2: Methanol oxidation protein MxaJ

MacromoleculeName: Methanol oxidation protein MxaJ / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methylorubrum extorquens (bacteria)
Molecular weightTheoretical: 32.468154 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLVNGRRRT AASVVALTAA LTALAALCAP AQAQDTKATS KAAEAAKPDA GTLRVCAAEQ PPLSMKDGSG LENRIATTVA EAMGRKAQF VWLGKPAIYL VRDGLEKKTC DVVIGLDADD PRVLTSKPYY RSGYVFLTRA DKDLDIKSWS DPRLKEVSHM V VGFGTPGE ...String:
MSLVNGRRRT AASVVALTAA LTALAALCAP AQAQDTKATS KAAEAAKPDA GTLRVCAAEQ PPLSMKDGSG LENRIATTVA EAMGRKAQF VWLGKPAIYL VRDGLEKKTC DVVIGLDADD PRVLTSKPYY RSGYVFLTRA DKDLDIKSWS DPRLKEVSHM V VGFGTPGE AMLKDIGRYE EDMAYLYSLV NFRAPRNQYT QIDPARMVSE VATGKAEVGV AFGPDVARYV RDSSTKLRMT PV PDDTQAS DGRKMPQSFD QAMGVRKDDT ALKAEIDAAL EKAKPKIEAI LKEEGVPVLP VSN

UniProtKB: Methanol oxidation protein MxaJ

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Macromolecule #3: PYRROLOQUINOLINE QUINONE

MacromoleculeName: PYRROLOQUINOLINE QUINONE / type: ligand / ID: 3 / Number of copies: 2 / Formula: PQQ
Molecular weightTheoretical: 330.206 Da
Chemical component information

ChemComp-PQQ:
PYRROLOQUINOLINE QUINONE

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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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120210
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER

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