9IY4 | pdb_00009iy4

Iterative acetyltransferase on lasso peptides from Actinomycetes in complex with AcCoA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9IY4

This is version 1.1 of the entry. See complete history

Literature

Iterative acylation on mature lasso peptides by widespread acetyltransferases.

Xiong, J.Wu, S.Liang, Z.Q.Fang, S.Tao, F.Y.Gong, X.T.Wu, X.Wu, Q.Cui, J.J.Gao, K.Hoi, K.K.Peng, Y.Luo, S.Lei, D.Dong, S.H.

(2026) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-026-02149-6
  • Primary Citation Related Structures: 
    9IY3, 9IY4, 9UBC

  • PubMed Abstract: 

    The biosynthesis of ribosomally synthesized and posttranslationally modified peptides (RiPPs) leverages iterative catalysis to enhance structural and biological diversity. Traditionally, iterative enzymes install posttranslational modifications on linear peptides, rather than mature RiPPs with intricate three-dimensional structures, which require complex changes in substrate binding. Here we present a prolific class of GCN5-related N-acetyltransferases (GNATs) that iteratively and consecutively acylate two Lys residues within the loop and ring motifs of lasso peptides, diverging from the typical iterative modification of linear peptides. Utilizing high-resolution cryogenic-electron microscopy and enzymatic reconstitution, we define the lasso peptide-binding pocket of IatT and pinpoint key residues that distinguish its two distinct acetylation steps. Structure-based engineering of IatT's acetyl-recognition site expands the cavity to accommodate longer-chain acyl groups, enabling the creation of lipolasso peptides, a class of ribosomal lipopeptide. This engineering strategy can be applied to any RiPP biosynthetic gene cluster encoding GNAT, facilitating the efficient diversification of ribosomal lipopeptides.


  • Organizational Affiliation
    • State Key Laboratory of Natural Product Chemistry, College of Chemistry and Chemical Engineering, School of Physical Science and Technology, Lanzhou University, Lanzhou, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 22.49 kDa 
  • Atom Count: 1,532 
  • Modeled Residue Count: 189 
  • Deposited Residue Count: 196 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GCN5-related N-acetyltransferase196Actinosynnema mirum DSM 43827Mutation(s): 0 
Gene Names: Amir_6318
UniProt
Find proteins for C6WJ45 (Actinosynnema mirum (strain ATCC 29888 / DSM 43827 / JCM 3225 / NBRC 14064 / NCIMB 13271 / NRRL B-12336 / IMRU 3971 / 101))
Explore C6WJ45 
Go to UniProtKB:  C6WJ45
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6WJ45
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO
(Subject of Investigation/LOI)

Query on ACO



Download:Ideal Coordinates CCD File
B [auth A]ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.2

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22077056
National Natural Science Foundation of China (NSFC)China22377046
National Natural Science Foundation of China (NSFC)China32171300
National Natural Science Foundation of China (NSFC)China2210070084
National Natural Science Foundation of China (NSFC)China21907046
Other government22ZD6FA006
Other government23ZDFA015

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release
  • Version 1.1: 2026-04-01
    Changes: Data collection, Database references