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- PDB-9iso: Cryo-EM structure of MxaF/MxaJ/PQQ complex -

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Basic information

Entry
Database: PDB / ID: 9iso
TitleCryo-EM structure of MxaF/MxaJ/PQQ complex
Components
  • Methanol dehydrogenase, alpha subunit
  • Methanol oxidation protein MxaJ
KeywordsPROTEIN BINDING / MxaF/MxaJ/PQQ
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
PYRROLOQUINOLINE QUINONE / Methanol dehydrogenase, alpha subunit / Methanol oxidation protein MxaJ
Similarity search - Component
Biological speciesMethylorubrum extorquens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsSun, J.Q. / Gao, F.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methanol dehydrogenase, alpha subunit
B: Methanol dehydrogenase, alpha subunit
C: Methanol oxidation protein MxaJ
D: Methanol oxidation protein MxaJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,2686
Polymers203,6084
Non-polymers6602
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Methanol dehydrogenase, alpha subunit


Mass: 69335.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens (bacteria) / Gene: mxaF, TK0001_1304 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1P8QPB7, Oxidoreductases; Acting on the CH-OH group of donors; With a cytochrome as acceptor
#2: Protein Methanol oxidation protein MxaJ


Mass: 32468.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens (bacteria) / Gene: mxaJ, TK0001_1306 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2N9AKP6
#3: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H6N2O8 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: MxaF/MxaJ/PQQ complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Methylorubrum extorquens (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120210 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313464
ELECTRON MICROSCOPYf_angle_d0.60218282
ELECTRON MICROSCOPYf_dihedral_angle_d4.9211844
ELECTRON MICROSCOPYf_chiral_restr0.0441920
ELECTRON MICROSCOPYf_plane_restr0.0052390

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