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- PDB-8y9g: Versatile Aromatic Prenyltransferase auraA in complex with DMSPP ... -

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Basic information

Entry
Database: PDB / ID: 8y9g
TitleVersatile Aromatic Prenyltransferase auraA in complex with DMSPP and cyclo-(L-Val-DH-His)
ComponentsVersatile Aromatic Prenyltransferase auraA
KeywordsTRANSFERASE / Prenyltransferase / Imidazole-Containing Diketopiperazines
Function / homology: / DIMETHYLALLYL S-THIOLODIPHOSPHATE
Function and homology information
Biological speciesPenicillium (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.67 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
DepositionFeb 6, 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)187,72012
Polymers185,7354
Non-polymers1,9868
Water724
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
Versatile Aromatic Prenyltransferase auraA


Mass: 46433.684 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium (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
#3: Chemical
ChemComp-A1LYF / (3~{Z},6~{S})-3-(1~{H}-imidazol-4-ylmethylidene)-6-propan-2-yl-piperazine-2,5-dione


Mass: 234.254 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H14N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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 in complex with DMSPP and cyclo-(L-Val-DH-His)
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Penicillium (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

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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 49.62 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 693975 / Symmetry type: POINT

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