7RC3 | pdb_00007rc3

Aeronamide N-methyltransferase, AerE (Y137F)

PDB DOI: https://doi.org/10.2210/pdb7RC3/pdb

Classification: TRANSFERASE
Organism(s): Microvirgula aerodenitrificans DSM 15089
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-07-07 Released: 2022-03-30
Deposition Author(s): Cogan, D.P., Reyes, R., Nair, S.K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free:
0.184 (Depositor), 0.187 (DCC)
R-Value Work:
0.164 (Depositor), 0.166 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2116578119
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 43.22 kDa
Atom Count: 3,456
Modeled Residue Count: 374
Deposited Residue Count: 384
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase family protein	A	384	Microvirgula aerodenitrificans DSM 15089	Mutation(s): 1
UniProt
Find proteins for A0A2S0PEL5 (Microvirgula aerodenitrificans) Explore A0A2S0PEL5 Go to UniProtKB: A0A2S0PEL5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2S0PEL5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ASP Query on ASP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]