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- PDB-9iy4: Iterative acetyltransferase on lasso peptides from Actinomycetes ... -

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Basic information

Entry
Database: PDB / ID: 9iy4
TitleIterative acetyltransferase on lasso peptides from Actinomycetes in complex with AcCoA
ComponentsGCN5-related N-acetyltransferase
KeywordsTRANSFERASE / GCN5-related N-acetyltransferases / Actinomycetes / AcCoA
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 / GCN5-related N-acetyltransferase
Function and homology information
Biological speciesActinosynnema mirum
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 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
DepositionJul 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4862
Polymers21,6761
Non-polymers8101
Water00
1
A: GCN5-related N-acetyltransferase
hetero molecules

A: GCN5-related N-acetyltransferase
hetero molecules

A: GCN5-related N-acetyltransferase
hetero molecules

A: GCN5-related N-acetyltransferase
hetero molecules

A: GCN5-related N-acetyltransferase
hetero molecules

A: GCN5-related N-acetyltransferase
hetero molecules

A: GCN5-related N-acetyltransferase
hetero molecules

A: GCN5-related N-acetyltransferase
hetero molecules

A: GCN5-related N-acetyltransferase
hetero molecules

A: GCN5-related N-acetyltransferase
hetero molecules

A: GCN5-related N-acetyltransferase
hetero molecules

A: GCN5-related N-acetyltransferase
hetero molecules

A: GCN5-related N-acetyltransferase
hetero molecules

A: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,80028
Polymers303,46614
Non-polymers11,33414
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation13
MethodUCSF CHIMERA

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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 (strain ATCC 29888 / DSM 43827 / JCM 3225 / NBRC 14064 / NCIMB 13271 / NRRL B-12336 / IMRU 3971 / 101) (bacteria)
Gene: Amir_6318 / Production host: Escherichia coli (E. coli) / References: UniProt: C6WJ45
#2: 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 modificationN

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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 and AcCoACOMPLEX#10MULTIPLE SOURCES
2Iterative acetyltransferaseCOMPLEX#11RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Actinosynnema mirum DSM 43827 (bacteria)446462
32Actinomycetes (high G+C Gram-positive bacteria)1760
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: FEI TITAN 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 software
IDNameVersionCategory
4CTFFIND4CTF correction
8PHENIXmodel refinement
10cryoSPARC4.2initial Euler assignment
11cryoSPARC4.2final Euler assignment
12cryoSPARC4.2classification
13cryoSPARC4.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D7 (2x7 fold dihedral)
3D reconstructionResolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4350000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0051571
ELECTRON MICROSCOPYf_angle_d0.6242144
ELECTRON MICROSCOPYf_dihedral_angle_d9.463226
ELECTRON MICROSCOPYf_chiral_restr0.045225
ELECTRON MICROSCOPYf_plane_restr0.005281

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