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TitleCryo-EM Detection of AMPylated Histidine Implies Covalent Catalysis in AMPylation Mediated by a Bacterial Effector.
Journal, issue, pagesJ Mol Biol, Vol. 437, Issue 3, Page 168917, Year 2025
Publish dateDec 16, 2024
AuthorsZhengrui Zhang / Rishi Patel / Zhao-Qing Luo / Chittaranjan Das /
PubMed AbstractAMPylation is a post-translational modification (PTM) whereby adenosine monophosphate (AMP) from adenosine triphosphate (ATP) is transferred onto protein hydroxyl groups of serine, threonine, or ...AMPylation is a post-translational modification (PTM) whereby adenosine monophosphate (AMP) from adenosine triphosphate (ATP) is transferred onto protein hydroxyl groups of serine, threonine, or tyrosine. Recently, an actin-dependent AMPylase namely LnaB from the bacterial pathogen Legionella pneumophila was found to AMPylate phosphate groups of phosphoribosylated ubiquitin and Src family kinases. LnaB represents an evolutionarily distinct family of AMPylases with conserved active site Ser-His-Glu residues. Here, we capture the structure of the LnaB-actin complex in a putative intermediate state via single-particle cryogenic electron microscopy (cryo-EM) and find that the catalytic histidine of LnaB is covalently attached to AMP through a phosphoramidate linkage at the Nδ1 atom. This observation provides direct structural evidence of histidine AMPylation as a PTM and implies the possibility of covalent catalysis in LnaB-mediated AMPylation, a mechanism distinct from known AMPylases. Subsequent biochemical studies confirm the observed AMP binding site and provide additional insights into the catalytic properties of LnaB. Together, our work highlights the power of cryo-EM in capturing labile PTMs and transient species during enzymatic reactions, while opening new avenues of mechanistic investigation into the LnaB family.
External linksJ Mol Biol / PubMed:39694182 / PubMed Central
MethodsEM (single particle)
Resolution2.83 Å
Structure data

44118

9b2z

EMDB-44118, PDB-9b2z:
Actin-bound Legionella pneumophila AMPylase LnaB with AMPylated catalytic histidine
Method: EM (single particle) / Resolution: 2.83 Å

Chemicals

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

ChemComp-CA:
Unknown entry

ChemComp-LAB:
LATRUNCULIN B / toxin*YM

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

Source
  • legionella pneumophila subsp. pneumophila str. philadelphia 1 (bacteria)
  • homo sapiens (human)
KeywordsTRANSFERASE / AMPylase / antitoxin / actin / ubiquitin

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