8V22 | pdb_00008v22

GlnA dodecamer with AMPylation

  • Classification: LIGASE
  • Organism(s): Escherichia coli
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-11-21 Released: 2024-11-27 
  • Deposition Author(s): Han, Y., Sreelatha, A., Gonzalez, A., Chen, Z.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), Cancer Prevention and Research Institute of Texas (CPRIT), Welch Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A repurposed AMP binding domain reveals mitochondrial protein AMPylation as a regulator of cellular metabolism.

Gonzalez, A.Pon, A.Servage, K.Pawlowski, K.Han, Y.Sreelatha, A.

(2025) Nat Commun 16: 7863-7863

  • DOI: https://doi.org/10.1038/s41467-025-63014-z
  • Primary Citation of Related Structures:  
    8V1Y, 8V22

  • PubMed Abstract: 

    Protein AMPylation, the covalent addition of adenosine monophosphate (AMP) to protein substrates, has been known as a post translational modification for over 50 years. Research in this field is largely underdeveloped due to the lack of tools that enable the systematic identification of AMPylated substrates. Here, we address this gap by developing an enrichment technique to isolate and study AMPylated proteins using a nucleotide-binding protein, hinT. Cryo-EM reconstruction of an AMPylated protein bound to hinT provides a structural basis for AMP selectivity. Using structure guided mutagenesis, we optimize enrichment to identify novel substrates of the evolutionarily conserved AMPylase, Selenoprotein O. We show that mammalian Selenoprotein O regulates metabolic flux through AMPylation of key mitochondrial proteins including glutamate dehydrogenase and pyruvate dehydrogenase. Our findings highlight the broader significance of AMPylation, an emerging post translational modification with critical roles in signal transduction and disease pathology. Furthermore, we establish a powerful enrichment platform for the discovery of novel AMPylated proteins to study the mechanisms and significance of protein AMPylation in cellular function.


  • Organizational Affiliation
    • Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine synthetase474Escherichia coliMutation(s): 0 
Gene Names: glnAb3870JW3841
EC: 6.3.1.2
UniProt
Find proteins for P0A9C5 (Escherichia coli (strain K12))
Explore P0A9C5 
Go to UniProtKB:  P0A9C5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9C5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
M [auth C]
N [auth D]
O [auth F]
P [auth H]
Q [auth I]
M [auth C],
N [auth D],
O [auth F],
P [auth H],
Q [auth I],
R [auth J],
S [auth L],
T [auth A],
U [auth B],
V [auth G],
W [auth E],
X [auth K]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0.1
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK123194
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRR190106
Welch FoundationUnited StatesI-2046-20200401
Welch FoundationUnited StatesI-2046-20230405

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Data collection, Database references