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- EMDB-44542: Salmonella undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose... -

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Basic information

Entry
Database: EMDB / ID: EMD-44542
TitleSalmonella undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase (ArnC) bound to UDP
Map data
Sample
  • Complex: ArnC homo tetramer with UDP
    • Protein or peptide: Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
  • Ligand: URIDINE-5'-DIPHOSPHATE
Keywordsmembrane protein / transferase / glycolipid biosynthesis / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homology
Function and homology information


undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase / undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase activity / 4-amino-4-deoxy-alpha-L-arabinopyranosyl undecaprenyl phosphate biosynthetic process / phosphotransferase activity, for other substituted phosphate groups / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / response to antibiotic / plasma membrane
Similarity search - Function
Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase / : / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGuo Y / Borek D / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Protein Sci / Year: 2025
Title: Cryo-EM SPR structures of Salmonella typhimurium ArnC; the key enzyme in lipid-A modification conferring polymyxin resistance.
Authors: Dhruvin H Patel / Elina Karimullina / Yirui Guo / Cameron Semper / Deepak T Patel / Tabitha Emde / Dominika Borek / Alexei Savchenko /
Abstract: Polymyxins are last-resort antimicrobial peptides administered clinically against multi-drug resistant bacteria, specifically in the case of Gram-negative species. However, an increasing number of ...Polymyxins are last-resort antimicrobial peptides administered clinically against multi-drug resistant bacteria, specifically in the case of Gram-negative species. However, an increasing number of these pathogens employ a defense strategy that involves a relay of enzymes encoded by the pmrE (ugd) loci and the arnBCDTEF operon. The pathway modifies the lipid-A component of the outer membrane (OM) lipopolysaccharide (LPS) by adding a 4-amino-4-deoxy-l-arabinose (L-Ara4N) headgroup, which renders polymyxins ineffective. Here, we report the cryo-EM SPR structures of glycosyltransferase ArnC from Salmonella typhimurium determined in apo and UDP-bound forms at resolutions 2.75 Å and 3.8 Å, respectively. The structure of the ArnC protomer comprises three distinct regions: an N-terminal glycosyltransferase domain, transmembrane region, and the interface helices (IHs). ArnC forms a tetramer with C2 symmetry, where the C-terminal strand inserts into the adjacent protomer. This tetrameric state is further stabilized by two distinct interfaces formed by ArnC that form a network of hydrogen bonds and salt bridges. The binding of UDP induces conformational changes that stabilize the loop between residues H201 to S213, and part of the putative catalytic pocket formed by IH1 and IH2. The surface property analysis revealed a hydrophobic cavity formed by TM1 and TM2 in the apo state, which is disrupted upon UDP binding. The comparison of ArnC structures to their homologs GtrB and DPMS suggests the key residues involved in ArnC catalytic activity.
History
DepositionApr 19, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44542.png

Downloads & links

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Map

FileDownload / File: emd_44542.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 300.24 Å		0.83 Å/pix.
x 360 pix.
= 300.24 Å		0.83 Å/pix.
x 360 pix.
= 300.24 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.115
Minimum - Maximum-0.12827216 - 0.27484065
Average (Standard dev.)0.0006655259 (±0.009926904)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 300.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_44542_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44542_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : ArnC homo tetramer with UDP

EntireName: ArnC homo tetramer with UDP
Components
  • Complex: ArnC homo tetramer with UDP
    • Protein or peptide: Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
  • Ligand: URIDINE-5'-DIPHOSPHATE

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Supramolecule #1: ArnC homo tetramer with UDP

SupramoleculeName: ArnC homo tetramer with UDP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Macromolecule #1: Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase

MacromoleculeName: Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 36.555238 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFDAAPIKKV SVVIPVYNEQ ESLPELIRRT TTACESLGKA WEILLIDDGS SDSSAELMVK ASQEADSHII SILLNRNYGQ HAAIMAGFS HVSGDLIITL DADLQNPPEE IPRLVAKADE GFDVVGTVRQ NRQDSLFRKS ASKIINLLIQ RTTGKAMGDY G CMLRAYRR ...String:
MFDAAPIKKV SVVIPVYNEQ ESLPELIRRT TTACESLGKA WEILLIDDGS SDSSAELMVK ASQEADSHII SILLNRNYGQ HAAIMAGFS HVSGDLIITL DADLQNPPEE IPRLVAKADE GFDVVGTVRQ NRQDSLFRKS ASKIINLLIQ RTTGKAMGDY G CMLRAYRR PIIDTMLRCH ERSTFIPILA NIFARRATEI PVHHAEREFG DSKYSFMRLI NLMYDLVTCL TTTPLRLLSL LG SVIAIGG FSLSVLLIVL RLALGPQWAA EGVFMLFAVL FTFIGAQFIG MGLLGEYIGR IYNDVRARPR YFVQQVIYPE STP FTEESH Q

UniProtKB: Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase

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Macromolecule #2: URIDINE-5'-DIPHOSPHATE

MacromoleculeName: URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: UDP
Molecular weightTheoretical: 404.161 Da
Chemical component information

ChemComp-UDP:
URIDINE-5'-DIPHOSPHATE / UDP*YM

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58569
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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