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- EMDB-60984: Iterative acetyltransferase on lasso peptides from Actinomycetes ... -

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Basic information

Entry
Database: EMDB / ID: EMD-60984
TitleIterative acetyltransferase on lasso peptides from Actinomycetes in complex with AcCoA
Map data
Sample
  • Complex: Complex of iterative acetyltransferase and AcCoA
    • Complex: Iterative acetyltransferase
      • Protein or peptide: GCN5-related N-acetyltransferase
  • Ligand: ACETYL COENZYME *A
KeywordsGCN5-related N-acetyltransferases / Actinomycetes / AcCoA / TRANSFERASE
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 / GCN5-related N-acetyltransferase
Function and homology information
Biological speciesActinosynnema mirum DSM 43827 (bacteria) / Actinomycetes (high G+C Gram-positive bacteria) / Actinosynnema mirum (strain ATCC 29888 / DSM 43827 / JCM 3225 / NBRC 14064 / NCIMB 13271 / NRRL B-12336 / IMRU 3971 / 101) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsWu S / Xiong J / Lei D / Dong S
Funding support China, 7 items
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
DepositionJul 29, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60984.png

Downloads & links

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Map

FileDownload / File: emd_60984.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.736 Å		0.83 Å/pix.
x 256 pix.
= 212.736 Å		0.83 Å/pix.
x 256 pix.
= 212.736 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.319
Minimum - Maximum-0.039043948 - 2.6327431
Average (Standard dev.)0.008993944 (±0.0937268)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.736 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60984_msk_1.map
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Half map: #2

Fileemd_60984_half_map_1.map
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Half map: #1

Fileemd_60984_half_map_2.map
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Sample components

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Entire : Complex of iterative acetyltransferase and AcCoA

EntireName: Complex of iterative acetyltransferase and AcCoA
Components
  • Complex: Complex of iterative acetyltransferase and AcCoA
    • Complex: Iterative acetyltransferase
      • Protein or peptide: GCN5-related N-acetyltransferase
  • Ligand: ACETYL COENZYME *A

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Supramolecule #1: Complex of iterative acetyltransferase and AcCoA

SupramoleculeName: Complex of iterative acetyltransferase and AcCoA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Actinosynnema mirum DSM 43827 (bacteria)

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Supramolecule #2: Iterative acetyltransferase

SupramoleculeName: Iterative acetyltransferase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Actinomycetes (high G+C Gram-positive bacteria)

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Macromolecule #1: GCN5-related N-acetyltransferase

MacromoleculeName: GCN5-related N-acetyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Actinosynnema mirum (strain ATCC 29888 / DSM 43827 / JCM 3225 / NBRC 14064 / NCIMB 13271 / NRRL B-12336 / IMRU 3971 / 101) (bacteria)
Molecular weightTheoretical: 21.676164 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSPQDDLIVW LRGDRAGLGP FSADLVDQYW RWEQDPSVLI GYGRQTPDSL ENRREGYGHQ ARGTDDQLRF TVYDLTGQDP VPVGTTAVL IDHHVRTGEF VIQLGAGHRG RGLGTEATRL TLDYAFHVSA LACVHLAVLT PNTGAIAAYE RAGFRRIGER R DSGFWLGR ...String:
MSPQDDLIVW LRGDRAGLGP FSADLVDQYW RWEQDPSVLI GYGRQTPDSL ENRREGYGHQ ARGTDDQLRF TVYDLTGQDP VPVGTTAVL IDHHVRTGEF VIQLGAGHRG RGLGTEATRL TLDYAFHVSA LACVHLAVLT PNTGAIAAYE RAGFRRIGER R DSGFWLGR RVSETLMDAV PEDFPGPSVV RGFVEGGR

UniProtKB: GCN5-related N-acetyltransferase

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Macromolecule #2: ACETYL COENZYME *A

MacromoleculeName: ACETYL COENZYME *A / type: ligand / ID: 2 / Number of copies: 1 / Formula: ACO
Molecular weightTheoretical: 809.571 Da
Chemical component information

ChemComp-ACO:
ACETYL COENZYME *A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 4350000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
FSC plot (resolution estimation)

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