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- PDB-8zgz: Cryo-EM structure of inward state Anhydromuropeptide permease (AmpG) -

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Basic information

Entry
Database: PDB / ID: 8zgz
TitleCryo-EM structure of inward state Anhydromuropeptide permease (AmpG)
ComponentsProtein AmpG
KeywordsTRANSPORT PROTEIN / antibiotic resistance / membrane transporter
Function / homology:
Function and homology information
Biological speciesYokenella regensburgei (Enteric Group 45)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsCho, H.S. / Kim, U. / Chang, N. / Kim, H. / Yoo, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Nat Commun / Year: 2025
Title: Structural and functional insights of AmpG in muropeptide transport and multiple β-lactam antibiotics resistance.
Authors: Nienping Chang / Hoyoung Kim / Uijin Kim / Yongju Cho / Youngki Yoo / Hyunsook Lee / Ji Won Kim / Min Sung Kim / Jaeho Lee / Young-Lag Cho / Kitae Kim / Dongeun Yong / Hyun-Soo Cho /
Abstract: Anhydromuropeptide permease (AmpG) is a transporter protein located in the inner membrane of certain gram -negative bacteria, involved in peptidoglycan (PG) recycling and β-lactamase induction. ...Anhydromuropeptide permease (AmpG) is a transporter protein located in the inner membrane of certain gram -negative bacteria, involved in peptidoglycan (PG) recycling and β-lactamase induction. Decreased AmpG function reduces resistance of antibiotic-resistant bacteria to β-lactam antibiotics. Therefore, AmpG-targeting inhibitors are promising 'antibiotic adjuvants'. However, as the tertiary structure of AmpG has not yet been identified, the development of targeted inhibitors remains challenging. We present four cryo-electron microscopy (cryo-EM) structures: the apo-inward and apo-outward state structures and the inward-occluded and outward states complexed with the substrate GlcNAc-1,6-anhMurNAc. Through functional analysis and molecular dynamics (MD) simulations, we identified motif A, which stabilizes the outward state, substrate-binding pocket, and protonation-related residues. Based on the structure of AmpG and our experimental results, we propose a muropeptide transport mechanism for AmpG. A deeper understanding of its structure and transport mechanism provides a foundation for the development of antibiotic adjuvants.
History
DepositionMay 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein AmpG


Theoretical massNumber of molelcules
Total (without water)54,0691
Polymers54,0691
Non-polymers00
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 Protein AmpG


Mass: 54069.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yokenella regensburgei (Enteric Group 45)
Gene: HMPREF0880_02314 / Production host: Escherichia coli (E. coli) / References: UniProt: G9Z488
Has protein modificationN

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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: AmpG, Anhydromuropeptide permease / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Yokenella regensburgei (Enteric Group 45)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil
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: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
7UCSF ChimeraX1.7model fitting
13PHENIXdev-4694model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86432 / Symmetry type: POINT
Atomic model buildingB value: 54.1 / Protocol: OTHER / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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