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- EMDB-60190: Cryo-EM structure of inward-facing Anhydromuropeptide permease (A... -

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Basic information

Entry
Database: EMDB / ID: EMD-60190
TitleCryo-EM structure of inward-facing Anhydromuropeptide permease (AmpG) in complex with GlcNAc-1,6-anhMurNAc
Map data
Sample
  • Complex: Cryo-EM structure ofAnhydromuropeptide permease (AmpG) complex with GlcNAc-1,6-anhMurNAc
    • Protein or peptide: Muropeptide transporter
  • Ligand: (2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-[(2S,3R,4R,5S,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6,8-dioxabicyclo[3.2.1]octan-3-yl]oxy]propanoic acid
KeywordsAmpG / MFS / Anhydromuropeptide permease / MEMBRANE PROTEIN
Function / homologyAmpG-like permease/Acetyl-coenzyme A transporter 1 / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Muropeptide transporter
Function and homology information
Biological speciesYokenella regensburgei (Enteric Group 45)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsChang N / Kim U / Yoo Y / Kim H / Cho H
Funding support1 items
OrganizationGrant numberCountry
Not funded
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 16, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60190.png

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Map

FileDownload / File: emd_60190.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 336 pix.
= 284.928 Å		0.85 Å/pix.
x 336 pix.
= 284.928 Å		0.85 Å/pix.
x 336 pix.
= 284.928 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.848 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.8948712 - 0.90786177
Average (Standard dev.)0.00044959714 (±0.010671194)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 284.928 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60190_msk_1.map
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Half map: #2

Fileemd_60190_half_map_1.map
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Half map: #1

Fileemd_60190_half_map_2.map
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Sample components

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Entire : Cryo-EM structure ofAnhydromuropeptide permease (AmpG) complex wi...

EntireName: Cryo-EM structure ofAnhydromuropeptide permease (AmpG) complex with GlcNAc-1,6-anhMurNAc
Components
  • Complex: Cryo-EM structure ofAnhydromuropeptide permease (AmpG) complex with GlcNAc-1,6-anhMurNAc
    • Protein or peptide: Muropeptide transporter
  • Ligand: (2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-[(2S,3R,4R,5S,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6,8-dioxabicyclo[3.2.1]octan-3-yl]oxy]propanoic acid

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Supramolecule #1: Cryo-EM structure ofAnhydromuropeptide permease (AmpG) complex wi...

SupramoleculeName: Cryo-EM structure ofAnhydromuropeptide permease (AmpG) complex with GlcNAc-1,6-anhMurNAc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Yokenella regensburgei (Enteric Group 45)

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Macromolecule #1: Muropeptide transporter

MacromoleculeName: Muropeptide transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yokenella regensburgei (Enteric Group 45)
Molecular weightTheoretical: 54.069086 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MANHYLRIFQ QPKSAILLIL GFASGLPLAL TSGTLQAWMT VENIDLKTIG FFSLVGQAYV FKFLWSPVMD RYTPPFLGRR RGWLVTTQI LLLIAIAAMG FLEPGTQLRW MAALAVVIAF CSASQDIVFD AWKTDVLPAE ERGTGAAISV LGYRLGMLVS G GLALWMAD ...String:
MANHYLRIFQ QPKSAILLIL GFASGLPLAL TSGTLQAWMT VENIDLKTIG FFSLVGQAYV FKFLWSPVMD RYTPPFLGRR RGWLVTTQI LLLIAIAAMG FLEPGTQLRW MAALAVVIAF CSASQDIVFD AWKTDVLPAE ERGTGAAISV LGYRLGMLVS G GLALWMAD KWLGWQGMYW LMAALLVPCI IATLLAPEPS DVVPVPRTLE QAVVAPLRDF FGRNNAWLIL LLIVLYKLGD AF AMSLTTT FLIRGVGFDA GEVGMVNKTL GLIATIIGAL YGGVLMQRLS LFRALLIFGI LQGVSNAGYW LLSITDKHLM SMA VAVFFE NLCGGMGTAA FVALLMTLCN KSFSATQFAL LSALSAVGRV YVGPIAGWFV EAHGWPTFYL FSVFAAVPGI LLLL ICRKT LEYTQQTESF MMRRHFSGAY QFALYLLLLG CLLLALWLIM LALNAIDYTS FSFLAGLLEV AALIAIAGVL LGAIL DYLA LRRTEEHKLA

UniProtKB: Muropeptide transporter

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Macromolecule #2: (2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-[(2S,3R,4R,5S,6R)-3-aceta...

MacromoleculeName: (2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-[(2S,3R,4R,5S,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6,8-dioxabicyclo[3.2.1]octan-3-yl]oxy]propanoic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: 2YP
Molecular weightTheoretical: 478.448 Da
Chemical component information

ChemComp-2YP:
(2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-[(2S,3R,4R,5S,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6,8-dioxabicyclo[3.2.1]octan-3-yl]oxy]propanoic acid

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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

Concentration9 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 67.0 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: 0.5 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133506
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC

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