[English] 日本語
Yorodumi
- EMDB-39074: Versatile Aromatic Prenyltransferase auraA in complex with DMAPP ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39074
TitleVersatile Aromatic Prenyltransferase auraA in complex with DMAPP and cyclo-(L-Val-L-His)
Map data
Sample
  • Complex: Versatile Aromatic Prenyltransferase auraA in complex with DMAPP and cyclo-(L-Val-L-His)
    • Protein or peptide: Versatile Aromatic Prenyltransferase auraA
  • Ligand: DIMETHYLALLYL S-THIOLODIPHOSPHATE
  • Ligand: (3~{S},6~{S})-3-(1~{H}-imidazol-4-ylmethyl)-6-propan-2-yl-piperazine-2,5-dione
  • Ligand: water
KeywordsPrenyltransferase / Imidazole-Containing Diketopiperazines / TRANSFERASE
Biological speciesPenicillium (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.45 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

-
Structure visualization

Supplemental images

emd_39074.png

Downloads & links

-
Map

FileDownload / File: emd_39074.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.427
Minimum - Maximum-2.9828289 - 3.989677
Average (Standard dev.)-0.00026931684 (±0.10293094)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #2

Fileemd_39074_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_39074_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Versatile Aromatic Prenyltransferase auraA in complex with DMAPP ...

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

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

SupramoleculeName: Versatile Aromatic Prenyltransferase auraA in complex with DMAPP and cyclo-(L-Val-L-His)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Penicillium (fungus)

-
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

-
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

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

MacromoleculeName: (3~{S},6~{S})-3-(1~{H}-imidazol-4-ylmethyl)-6-propan-2-yl-piperazine-2,5-dione
type: ligand / ID: 3 / Number of copies: 4 / Formula: A1LYE
Molecular weightTheoretical: 236.27 Da

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.45 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

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1345019
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more