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- EMDB-65981: cryo-EM structure of E.coli ArnA -

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Basic information

Entry
Database: EMDB / ID: EMD-65981
Titlecryo-EM structure of E.coli ArnA
Map data
Sample
  • Cell: Bifunctional polymyxin resistance protein ArnA
    • Protein or peptide: Bifunctional polymyxin resistance protein ArnA
KeywordsBifunctional polymyxin resistance protein ArnA / ANTIBIOTIC
Function / homology
Function and homology information


UDP-4-deoxy-4-formamido-beta-L-arabinopyranose biosynthetic process / UDP-glucuronate dehydrogenase activity / UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity / UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating) / UDP-4-amino-4-deoxy-L-arabinose formyltransferase / UDP-D-xylose biosynthetic process / UDP-glucuronate decarboxylase activity / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / NAD+ binding ...UDP-4-deoxy-4-formamido-beta-L-arabinopyranose biosynthetic process / UDP-glucuronate dehydrogenase activity / UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity / UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating) / UDP-4-amino-4-deoxy-L-arabinose formyltransferase / UDP-D-xylose biosynthetic process / UDP-glucuronate decarboxylase activity / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / NAD+ binding / response to antibiotic / protein-containing complex / identical protein binding / membrane
Similarity search - Function
Bifunctional polymyxin resistance protein, ArnA / Bifunctional polymyxin resistance protein ArnA-like, extended (e) SDRs / : / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / NAD-dependent epimerase/dehydratase ...Bifunctional polymyxin resistance protein, ArnA / Bifunctional polymyxin resistance protein ArnA-like, extended (e) SDRs / : / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Bifunctional polymyxin resistance protein ArnA
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsLiu X / Li J
Funding support China, 1 items
OrganizationGrant numberCountry
Other government23700-52531020 China
CitationJournal: Biomolecules / Year: 2025
Title: Structural Basis for Targeting the Bifunctional Enzyme ArnA.
Authors: Xinyu Liu / Ruochen Yang / Libang Ren / Tong Li / Yanrong Li / Zhihua Yan / Yanrong Gao / Mingqi Yang / Jiazhi Li /
Abstract: Polymyxin antibiotics are often the last line of defense against multidrug-resistant Gram-negative pathogens. A key resistance mechanism involves the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) ...Polymyxin antibiotics are often the last line of defense against multidrug-resistant Gram-negative pathogens. A key resistance mechanism involves the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) to lipid A, mediated by the bifunctional enzyme ArnA. However, the evolutionary rationale and structural basis for ArnA's domain fusion, hexameric assembly, and catalytic coordination remain mechanistically unresolved. Here, we integrate evolutionary genomics, high-resolution cryo-electron microscopy (cryo-EM), and computational protein design to provide a comprehensive mechanistic analysis of ArnA. Our evolutionary analysis reveals that the dehydrogenase (DH) and formyltransferase (TF) domains evolved independently and were selectively fused in Gammaproteobacteria, suggesting an adaptive advantage. A 2.89 Å cryo-EM structure of apo-ArnA resolves the flexible interdomain linker and reveals a DH-driven hexameric architecture essential for enzymatic activity. 3D variability analysis captures intrinsic conformational dynamics, indicating a molecular switch that may coordinate sequential catalysis and substrate channeling. Structure-based peptide inhibitors targeting the hexamerization and predicted ArnA-ArnB interaction interfaces were computationally designed, offering a novel strategy for disrupting L-Ara4N biosynthesis. These findings illuminate a previously uncharacterized structural mechanism of antimicrobial resistance and lay the groundwork for therapeutic intervention.
History
DepositionAug 27, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65981.png

Downloads & links

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Map

FileDownload / File: emd_65981.map.gz / Format: CCP4 / Size: 216 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.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.873387 - 1.4383063
Average (Standard dev.)-0.00028823907 (±0.026688704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65981_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_65981_half_map_2.map
Projections & Slices
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Sample components

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Entire : Bifunctional polymyxin resistance protein ArnA

EntireName: Bifunctional polymyxin resistance protein ArnA
Components
  • Cell: Bifunctional polymyxin resistance protein ArnA
    • Protein or peptide: Bifunctional polymyxin resistance protein ArnA

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Supramolecule #1: Bifunctional polymyxin resistance protein ArnA

SupramoleculeName: Bifunctional polymyxin resistance protein ArnA / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli BW25113 (bacteria)

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Macromolecule #1: Bifunctional polymyxin resistance protein ArnA

MacromoleculeName: Bifunctional polymyxin resistance protein ArnA / type: protein_or_peptide / ID: 1
Details: Sequence reference for Escherichia coli BW25113 is not available at the time of biocuration. Current sequence reference is from UniProt ID P77398.
Number of copies: 6 / Enantiomer: LEVO
EC number: UDP-4-amino-4-deoxy-L-arabinose formyltransferase
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 74.385773 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKTVVFAYHD MGCLGIEALL AAGYEISAIF THTDNPGEKA FYGSVARLAA ERGIPVYAPD NVNHPLWVER IAQLSPDVIF SFYYRHLIY DEILQLAPAG AFNLHGSLLP KYRGRAPLNW VLVNGETETG VTLHRMVKRA DAGAIVAQLR IAIAPDDIAI T LHHKLCHA ...String:
MKTVVFAYHD MGCLGIEALL AAGYEISAIF THTDNPGEKA FYGSVARLAA ERGIPVYAPD NVNHPLWVER IAQLSPDVIF SFYYRHLIY DEILQLAPAG AFNLHGSLLP KYRGRAPLNW VLVNGETETG VTLHRMVKRA DAGAIVAQLR IAIAPDDIAI T LHHKLCHA ARQLLEQTLP AIKHGNILEI AQRENEATCF GRRTPDDSFL EWHKPASVLH NMVRAVADPW PGAFSYVGNQ KF TVWSSRV HPHASKAQPG SVISVAPLLI ACGDGALEIV TGQAGDGITM QGSQLAQTLG LVQGSRLNSQ PACTARRRTR VLI LGVNGF IGNHLTERLL REDHYEVYGL DIGSDAISRF LNHPHFHFVE GDISIHSEWI EYHVKKCDVV LPLVAIATPI EYTR NPLRV FELDFEENLR IIRYCVKYRK RIIFPSTSEV YGMCSDKYFD EDHSNLIVGP VNKPRWIYSV SKQLLDRVIW AYGEK EGLQ FTLFRPFNWM GPRLDNLNAA RIGSSRAITQ LILNLVEGSP IKLIDGGKQK RCFTDIRDGI EALYRIIENA GNRCDG EII NIGNPENEAS IEELGEMLLA SFEKHPLRHH FPPFAGFRVV ESSSYYGKGY QDVEHRKPSI RNAHRCLDWE PKIDMQE TI DETLDFFLRT VDLTDKPS

UniProtKB: Bifunctional polymyxin resistance protein ArnA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Number grids imaged: 1 / Number real images: 6563 / 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: 1.8 µm / Nominal defocus min: 1.1 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 476403
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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