9ASC | pdb_00009asc

Cryo-EM Structure of the Glycosyltransferase ArnC from Salmonella enterica in the UDP-bound State Determined on Talos Arctica microscope


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of undecaprenyl phosphate glycosylation leading to polymyxin resistance in Gram-negative bacteria.

Ashraf, K.U.Bunoro-Batista, M.Ansell, T.B.Punetha, A.Rosario-Garrido, S.Firlar, E.Kaelber, J.T.Stansfeld, P.J.Petrou, V.I.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.01.29.634835
  • Primary Citation of Related Structures:  
    8VXH, 9ASC, 9B77

  • PubMed Abstract: 

    In Gram-negative bacteria, the enzymatic modification of Lipid A with aminoarabinose (L-Ara4N) leads to resistance against polymyxin antibiotics and cationic antimicrobial peptides. ArnC, an integral membrane glycosyltransferase, attaches a formylated form of aminoarabinose to the lipid undecaprenyl phosphate, enabling its association with the bacterial inner membrane. Here, we present cryo-electron microscopy structures of ArnC from S. enterica in apo and nucleotide-bound conformations. These structures reveal a conformational transition that takes place upon binding of the partial donor substrate. Using coarse-grained and atomistic simulations, we provide insights into substrate coordination before and during catalysis, and we propose a catalytic mechanism that may operate on all similar metal-dependent polyprenyl phosphate glycosyltransferases. The reported structures provide a new target for drug design aiming to combat polymyxin resistance.


  • Organizational Affiliation

    Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
A, B, C, D
363Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 0 
Gene Names: arnCpbgP2pmrFSTM2298
EC: 2.4.2.53
Membrane Entity: Yes 
UniProt
Find proteins for O52324 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore O52324 
Go to UniProtKB:  O52324
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO52324
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP (Subject of Investigation/LOI)
Query on UDP

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487
RECONSTRUCTIONcryoSPARC3.3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR00GM123228
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM150831

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-02-12
    Changes: Data collection, Database references
  • Version 1.2: 2025-03-05
    Changes: Data collection, Database references