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- EMDB-61491: Versatile Aromatic Prenyltransferase auraA mutant-Y207A in comple... -

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Entry
Database: EMDB / ID: EMD-61491
TitleVersatile Aromatic Prenyltransferase auraA mutant-Y207A in complex with DMSPP
Map data
Sample
  • Complex: Versatile Aromatic Prenyltransferase auraA mutant-Y207A in complex with DMSPP
    • Protein or peptide: Versatile Aromatic Prenyltransferase auraA
  • Ligand: DIMETHYLALLYL S-THIOLODIPHOSPHATE
KeywordsPrenyltransferase / Imidazole-Containing Diketopiperazines / TRANSFERASE
Biological speciesPenicillium solitum (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsLi D / Zhang Y / Wang W / Wang P
Funding support China, 3 items
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, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61491.png

Downloads & links

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Map

FileDownload / File: emd_61491.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 192 pix.
= 227.84 Å		1.19 Å/pix.
x 192 pix.
= 227.84 Å		1.19 Å/pix.
x 192 pix.
= 227.84 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.18667 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.8727317 - 2.7070537
Average (Standard dev.)0.00001415551 (±0.07877707)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 227.83997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61491_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_61491_half_map_2.map
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Sample components

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Entire : Versatile Aromatic Prenyltransferase auraA mutant-Y207A in comple...

EntireName: Versatile Aromatic Prenyltransferase auraA mutant-Y207A in complex with DMSPP
Components
  • Complex: Versatile Aromatic Prenyltransferase auraA mutant-Y207A in complex with DMSPP
    • Protein or peptide: Versatile Aromatic Prenyltransferase auraA
  • Ligand: DIMETHYLALLYL S-THIOLODIPHOSPHATE

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Supramolecule #1: Versatile Aromatic Prenyltransferase auraA mutant-Y207A in comple...

SupramoleculeName: Versatile Aromatic Prenyltransferase auraA mutant-Y207A in complex with DMSPP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Penicillium solitum (fungus)

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Macromolecule #1: Versatile Aromatic Prenyltransferase auraA

MacromoleculeName: Versatile Aromatic Prenyltransferase auraA / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Penicillium solitum (fungus)
Molecular weightTheoretical: 48.883469 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTVEHAQLTS NDLLVKSISS SPSPSPWDFL GRVLQFQHGD HKRWWDVLAP VFGISMASIG YKLDVQYRHL LVLYDAVIPN MGPFPNSNA SNITWTSPFP PGPLEASVNY QAGESSMFRF TIEPVGPHAG TPADPVNELA AKQLMQRLGQ LQPGGVDSTM F DHFYPLLC ...String:
MTVEHAQLTS NDLLVKSISS SPSPSPWDFL GRVLQFQHGD HKRWWDVLAP VFGISMASIG YKLDVQYRHL LVLYDAVIPN MGPFPNSNA SNITWTSPFP PGPLEASVNY QAGESSMFRF TIEPVGPHAG TPADPVNELA AKQLMQRLGQ LQPGGVDSTM F DHFYPLLC VDGPEARRQW DSIAHIYHKC HTVTALDMQR SAACTLKTAF PPLLRSTIMN TSMVDIMFDA VESFRKQSGL YF DYTKIKE FMSEEKTHET MMVDRSYLSF DCLDPAKSRI KIYTEAKVKT LEEAYSFWSL GGRLSGPEID YGFKIVSQMW DAI YSKELP GGKQRENNHI QINWEMSAKD SSVAPKLYLT VIEDYDAYVS SAIVDLFTGL GWAAHVQTHK KIEKEAYPMC DANP QSTHA YVWISLAYKK TGPYITVYTN PGASILEKA

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Macromolecule #2: DIMETHYLALLYL S-THIOLODIPHOSPHATE

MacromoleculeName: DIMETHYLALLYL S-THIOLODIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: DST
Molecular weightTheoretical: 262.158 Da
Chemical component information

ChemComp-DST:
DIMETHYLALLYL S-THIOLODIPHOSPHATE

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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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 178786
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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