7RC6

Aeronamide N-methyltransferase, AerE, bound to modified peptide substrate, AerA-DL,34

• PDB DOI: https://doi.org/10.2210/pdb7RC6/pdb

• Classification: TRANSFERASE/BIOSYNTHETIC PROTEIN
• Organism(s): Microvirgula aerodenitrificans DSM 15089
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-07-07 Released: 2022-03-30 
• Deposition Author(s): Cogan, D.P., Reyes, R., Nair, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.188 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Literature

Structure and mechanism for iterative amide N -methylation in the biosynthesis of channel-forming peptide cytotoxins.

Cogan, D.P., Bhushan, A., Reyes, R., Zhu, L., Piel, J., Nair, S.K.

(2022) Proc Natl Acad Sci U S A 119: e2116578119-e2116578119

• PubMed: 35316135 
• DOI: https://doi.org/10.1073/pnas.2116578119
• Primary Citation of Related Structures:  
  7RC2, 7RC3, 7RC4, 7RC5, 7RC6


• PubMed Abstract: 
  

  SignificanceThe channel-forming proteusins are bacterial helical peptides that allow permeation of positively charged ions to influence membrane potential and cellular physiology. We biochemically characterize the effect of two critical posttranslational modifications on the secondary structure of the peptide substrate. We determine how a methyl group can be added to the side chains of D-Asn residues in a peptide substrate and show how flanking residues influence selectivity. These studies should foster the development of small-molecule peptide ion channels as therapeutics.

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Organizational Affiliation: 

Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.47 kDa 
• Atom Count: 3,571 
• Modelled Residue Count: 386 
• Deposited Residue Count: 418 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase family protein	A	384	Microvirgula aerodenitrificans DSM 15089	Mutation(s): 0  Gene Names: aerE
UniProt
Find proteins for A0A2S0PEL5 (Microvirgula aerodenitrificans) Explore A0A2S0PEL5  Go to UniProtKB:  A0A2S0PEL5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aeronamide A peptide	B [auth C]	34	Microvirgula aerodenitrificans DSM 15089	Mutation(s): 0  Gene Names: aerA

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	D [auth C]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
NA (Subject of Investigation/LOI)	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.188 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.029	α = 90
b = 78.029	β = 90
c = 153.399	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-03-30 
Deposition Author(s): Cogan, D.P., Reyes, R., Nair, S.K.

Revision History  

• Version 1.0: 2022-03-30
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection