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- PDB-9jhx: Versatile Aromatic Prenyltransferase auraA mutant-Y207A in comple... -

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Entry
Database: PDB / ID: 9jhx
TitleVersatile Aromatic Prenyltransferase auraA mutant-Y207A in complex with DMSPP
ComponentsVersatile Aromatic Prenyltransferase auraA
KeywordsTRANSFERASE / Prenyltransferase / Imidazole-Containing Diketopiperazines
Function / homologyDIMETHYLALLYL S-THIOLODIPHOSPHATE
Function and homology information
Biological speciesPenicillium solitum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsLi, D. / Zhang, Y. / Wang, W. / Wang, P.
Funding support China, 3items
OrganizationGrant numberCountry
Other governmentHainan Provincial Joint Project of Sanya Yazhou Bay Science and Technology City (Grant No: 2021CXLH0012) China
Other governmentMajor Basic Research Programs of Natural Science Foundation of Shandong Province (ZR2019ZD18) China
Other governmentQingdao Marine Science and Technology Center (No.2022QNLM030003-1) China
CitationJournal: Nat Commun / Year: 2025
Title: Characterization and structural analysis of a versatile aromatic prenyltransferase for imidazole-containing diketopiperazines.
Authors: Wenxue Wang / Peng Wang / Chuanteng Ma / Kang Li / Zian Wang / Yuting Liu / Lu Wang / Guojian Zhang / Qian Che / Tianjiao Zhu / Yuzhong Zhang / Dehai Li /
Abstract: Prenylation modifications of natural products play essential roles in chemical diversity and bioactivities, but imidazole modification prenyltransferases are not well investigated. Here, we discover ...Prenylation modifications of natural products play essential roles in chemical diversity and bioactivities, but imidazole modification prenyltransferases are not well investigated. Here, we discover a dimethylallyl tryptophan synthase family prenyltransferase, AuraA, that catalyzes the rare dimethylallylation on the imidazole moiety in the biosynthesis of aurantiamine. Biochemical assays validate that AuraA could accept both cyclo-(L-Val-L-His) and cyclo-(L-Val-DH-His) as substrates, while the prenylation modes are completely different, yielding C2-regular and C5-reverse products, respectively. Cryo-electron microscopy analysis of AuraA and its two ternary complex structures reveal two distinct modes for receptor binding, demonstrating a tolerance for altered orientations of highly similar receptors. The mutation experiments further demonstrate the promiscuity of AuraA towards imidazole-C-dimethylallylation. In this work, we also characterize a case of AuraA mutant-catalyzed dimethylallylation of imidazole moiety, offering available structural insights into the utilization and engineering of dimethylallyl tryptophan synthase family prenyltransferases.
History
DepositionSep 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Versatile Aromatic Prenyltransferase auraA
B: Versatile Aromatic Prenyltransferase auraA
C: Versatile Aromatic Prenyltransferase auraA
D: Versatile Aromatic Prenyltransferase auraA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,5838
Polymers195,5344
Non-polymers1,0494
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Versatile Aromatic Prenyltransferase auraA


Mass: 48883.469 Da / Num. of mol.: 4 / Mutation: Y207A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium solitum (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O6P2S / 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

ComponentName: Versatile Aromatic Prenyltransferase auraA mutant-Y207A in complex with DMSPP
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Penicillium solitum (fungus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (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

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178786 / Symmetry type: POINT

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