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- PDB-9ubc: Sub-particle structure of the iterative acetyltransferase from Ac... -

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Basic information

Entry
Database: PDB / ID: 9ubc
TitleSub-particle structure of the iterative acetyltransferase from Actinomycetes in complex with AcCoA and monoacetylated lasso peptides
Components
  • Albusnodin family lasso peptide
  • GCN5-related N-acetyltransferase
KeywordsTRANSFERASE / GCN5-related N-acetyltransferases / Actinomycetes / AcCoA / Lasso peptides
Function / homologyAcetyltransferase (GNAT) domain / acyltransferase activity, transferring groups other than amino-acyl groups / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / ACETYL COENZYME *A / Albusnodin family lasso peptide / GCN5-related N-acetyltransferase
Function and homology information
Biological speciesActinosynnema mirum DSM 43827 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsWu, S. / Xiong, J. / Lei, D. / Dong, S.
Funding support China, 7items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077056 China
National Natural Science Foundation of China (NSFC)22377046 China
National Natural Science Foundation of China (NSFC)32171300 China
National Natural Science Foundation of China (NSFC)2210070084 China
National Natural Science Foundation of China (NSFC)21907046 China
Other government22ZD6FA006
Other government23ZDFA015
CitationJournal: Nat Chem Biol / Year: 2026
Title: Iterative acylation on mature lasso peptides by widespread acetyltransferases.
Authors: Jiang Xiong / Shanquan Wu / Zi-Qi Liang / Shuo Fang / Fen-Yu Tao / Xiao-Tong Gong / Xing Wu / Qingfeng Wu / Jiao-Jiao Cui / Kun Gao / Kin Kuan Hoi / Yong Peng / Shangwen Luo / Dongsheng Lei / Shi-Hui Dong /
Abstract: The biosynthesis of ribosomally synthesized and posttranslationally modified peptides (RiPPs) leverages iterative catalysis to enhance structural and biological diversity. Traditionally, iterative ...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.
History
DepositionApr 2, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GCN5-related N-acetyltransferase
C: Albusnodin family lasso peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1683
Polymers23,3582
Non-polymers8101
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein GCN5-related N-acetyltransferase


Mass: 21676.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinosynnema mirum DSM 43827 (bacteria)
Gene: Amir_6318 / Production host: Escherichia coli (E. coli) / References: UniProt: C6WJ45
#2: Protein/peptide Albusnodin family lasso peptide


Mass: 1681.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinosynnema mirum DSM 43827 (bacteria)
Gene: FHR32_000276 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7W7W6P0
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of iterative acetyltransferase, AcCoA and monoacetylated lasso peptidesCOMPLEX#1-#20MULTIPLE SOURCES
2Iterative acetyltransferaseCOMPLEX#11RECOMBINANT
3monoacetylated lasso peptidesCOMPLEX#21RECOMBINANT
Source (natural)Organism: Actinosynnema mirum DSM 43827 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78368 / Symmetry type: POINT
RefinementHighest resolution: 3.43 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0021688
ELECTRON MICROSCOPYf_angle_d0.4472296
ELECTRON MICROSCOPYf_dihedral_angle_d11.245605
ELECTRON MICROSCOPYf_chiral_restr0.038237
ELECTRON MICROSCOPYf_plane_restr0.003303

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