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- EMDB-39079: Versatile Aromatic Prenyltransferase auraA in complex with DMSPP ... -

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Basic information

Entry
Database: EMDB / ID: EMD-39079
TitleVersatile Aromatic Prenyltransferase auraA in complex with DMSPP and cyclo-(L-Val-DH-His)
Map data
Sample
  • Complex: Versatile Aromatic Prenyltransferase auraA in complex with DMSPP and cyclo-(L-Val-DH-His)
    • Protein or peptide: Versatile Aromatic Prenyltransferase auraA
  • Ligand: DIMETHYLALLYL S-THIOLODIPHOSPHATE
  • Ligand: (3~{Z},6~{S})-3-(1~{H}-imidazol-4-ylmethylidene)-6-propan-2-yl-piperazine-2,5-dione
  • Ligand: water
KeywordsPrenyltransferase / Imidazole-Containing Diketopiperazines / TRANSFERASE
Biological speciesPenicillium (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 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
DepositionFeb 6, 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_39079.png

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Map

FileDownload / File: emd_39079.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.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.427
Minimum - Maximum-3.0255299 - 3.8480692
Average (Standard dev.)-0.00073649804 (±0.097729556)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39079_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_39079_half_map_2.map
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Sample components

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Entire : Versatile Aromatic Prenyltransferase auraA in complex with DMSPP ...

EntireName: Versatile Aromatic Prenyltransferase auraA in complex with DMSPP and cyclo-(L-Val-DH-His)
Components
  • Complex: Versatile Aromatic Prenyltransferase auraA in complex with DMSPP and cyclo-(L-Val-DH-His)
    • Protein or peptide: Versatile Aromatic Prenyltransferase auraA
  • Ligand: DIMETHYLALLYL S-THIOLODIPHOSPHATE
  • Ligand: (3~{Z},6~{S})-3-(1~{H}-imidazol-4-ylmethylidene)-6-propan-2-yl-piperazine-2,5-dione
  • Ligand: water

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Supramolecule #1: Versatile Aromatic Prenyltransferase auraA in complex with DMSPP ...

SupramoleculeName: Versatile Aromatic Prenyltransferase auraA in complex with DMSPP and cyclo-(L-Val-DH-His)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Penicillium (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 (fungus)
Molecular weightTheoretical: 46.433684 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SPSPWDFLGR VLQFQHGDHK RWWDVLAPVF GISMASIGYK LDVQYRHLLV LYDAVIPNMG PFPNSNASNI TWTSPFPPGP LEASVNYQA GESSMFRFTI EPVGPHAGTP ADPVNELAAK QLMQRLGQLQ PGGVDSTMFD HFYPLLCVDG PEARRQWDSI A HIYHKCHT ...String:
SPSPWDFLGR VLQFQHGDHK RWWDVLAPVF GISMASIGYK LDVQYRHLLV LYDAVIPNMG PFPNSNASNI TWTSPFPPGP LEASVNYQA GESSMFRFTI EPVGPHAGTP ADPVNELAAK QLMQRLGQLQ PGGVDSTMFD HFYPLLCVDG PEARRQWDSI A HIYHKCHT VTALDMQRSA ACTLKTYFPP LLRSTIMNTS MVDIMFDAVE SFRKQSGLYF DYTKIKEFMS EEKTHETMMV DR SYLSFDC LDPAKSRIKI YTEAKVKTLE EAYSFWSLGG RLSGPEIDYG FKIVSQMWDA IYSKELPGGK QRENNHIQIN WEM SAKDSS VAPKLYLTVI EDYDAYVSSA IVDLFTGLGW AAHVQTHKKI EKEAYPMCDA NPQSTHAYVW ISLAYKKTGP YITV YTNPG ASILE

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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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Macromolecule #3: (3~{Z},6~{S})-3-(1~{H}-imidazol-4-ylmethylidene)-6-propan-2-yl-pi...

MacromoleculeName: (3~{Z},6~{S})-3-(1~{H}-imidazol-4-ylmethylidene)-6-propan-2-yl-piperazine-2,5-dione
type: ligand / ID: 3 / Number of copies: 4 / Formula: A1LYF
Molecular weightTheoretical: 234.254 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 BIOQUANTUM (6k x 4k) / Average electron dose: 49.62 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 693975
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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