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- PDB-9c4o: Cryo-EM structure of PqqU with ligand PQQ -

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Basic information

Entry
Database: PDB / ID: 9c4o
TitleCryo-EM structure of PqqU with ligand PQQ
ComponentsPyrroloquinoline quinone transporter
KeywordsMEMBRANE PROTEIN / TonD-dependent / outer membrane / transporter / PQQ uptake
Function / homology
Function and homology information


siderophore transmembrane transport / intracellular monoatomic cation homeostasis / siderophore uptake transmembrane transporter activity / transmembrane transporter complex / cell outer membrane / signaling receptor activity / membrane
Similarity search - Function
: / TonB-dependent siderophore receptor / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily
Similarity search - Domain/homology
PYRROLOQUINOLINE QUINONE / Pyrroloquinoline quinone transporter
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.99 Å
AuthorsMunder, F. / Venugopal, H. / Grinter, R.
Funding support Australia, 4items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1197376 Australia
Australian Research Council (ARC)DP230102150 Australia
Australian Research Council (ARC)LE200100045 Australia
Australian Research Council (ARC)LE120100090 Australia
CitationJournal: Sci Adv / Year: 2025
Title: High-affinity PQQ import is widespread in Gram-negative bacteria.
Authors: Fabian Munder / Marcos Voutsinos / Klaus Hantke / Hari Venugopal / Rhys Grinter /
Abstract: Pyrroloquinoline quinone (PQQ) is a soluble redox cofactor used by diverse bacteria. Many Gram-negative bacteria that encode PQQ-dependent enzymes do not produce it and instead obtain it from the ...Pyrroloquinoline quinone (PQQ) is a soluble redox cofactor used by diverse bacteria. Many Gram-negative bacteria that encode PQQ-dependent enzymes do not produce it and instead obtain it from the environment. To achieve this, uses the TonB-dependent transporter PqqU as a high-affinity PQQ importer. Here, we show that PqqU binds PQQ with high affinity and determine the high-resolution structure of the PqqU-PQQ complex, revealing that PqqU undergoes conformational changes in PQQ binding to capture the cofactor in an internal cavity. We show that these conformational changes preclude the binding of a bacteriophage, which targets PqqU as a cell surface receptor. Guided by the PqqU-PQQ structure, we identify amino acids essential for PQQ import and leverage this information to map the presence of PqqU across Gram-negative bacteria. This reveals that PqqU is encoded by Gram-negative bacteria from at least 22 phyla occupying diverse habitats, indicating that PQQ is an important cofactor for bacteria that adopt diverse lifestyles and metabolic strategies.
History
DepositionJun 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.0Jun 19, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 19, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2May 28, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name
Revision 1.3Jun 11, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.4Aug 13, 2025Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrroloquinoline quinone transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7713
Polymers78,4011
Non-polymers3702
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Pyrroloquinoline quinone transporter / PQQ transporter / TonB-dependent receptor PqqU


Mass: 78401.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Gene: pqqU, yncD, b1451, JW1446 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P76115
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H6N2O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
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: Complex of PqqU with PQQ / Type: COMPLEX
Details: TonB-dependent outer membrane transporter PqqU in complex with its substrate PQQ.
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.078 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
Details: LMNG was partly removed by concentration in a 100 kDa cut-off concentrator.
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HClC4H11NO31
2150 mMSodium ChlorideNaCl1
30.025 %Lauryl Maltose Neopentyl GlycolC47H88O221
SpecimenConc.: 3.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 30 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: 3 microliters of sample

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5.22 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of real images: 8744
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1RELION4.0.1particle selection
2EPUimage acquisition
8PHENIXmodel refinement
12cryoSPARC4.2.0classification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2110000
3D reconstructionResolution: 1.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 872884 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045287
ELECTRON MICROSCOPYf_angle_d0.6087177
ELECTRON MICROSCOPYf_dihedral_angle_d6.427743
ELECTRON MICROSCOPYf_chiral_restr0.044745
ELECTRON MICROSCOPYf_plane_restr0.005958

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