9V4I | pdb_00009v4i

Prenyltransferase Ord1 D219A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.254 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure-Activity Relationship of an All-alpha-helical Prenyltransferase Reveals the Mechanism of Indole Prenylation.

Oshiro, T.Uehara, S.Suto, A.Tanaka, Y.Ito, T.Kodera, Y.Matsui, T.

(2025) Biochemistry 

  • DOI: https://doi.org/10.1021/acs.biochem.5c00329
  • Primary Citation of Related Structures:  
    9V4G, 9V4H, 9V4I, 9V4J

  • PubMed Abstract: 

    Enzymes are involved in the biosynthesis of a variety of secondary metabolites found in nature. The catalytic mechanism is regulated by the three-dimensional structure of the enzyme, particularly at the catalytic site, resulting in the synthesis of natural products with complex conformations derived from a regioselective, chemoselective, or stereoselective preference of the enzyme reaction. Prenyltransferase, which belongs to the prenylsynthase superfamily, catalyzes the condensation of isoprene to an aromatic compound, consequently producing a terpenoid scaffold structure. Prenyltransferase thus plays an important role in expanding the chemical diversity of the terpenoids. Although the three-dimensional structures of prenylsynthases categorized in the same superfamily have been resolved, the catalytic mechanism of prenyltransferase has been veiled. In this study, we determined the X-ray crystal structure of a novel prenyltransferase, Ord1, which is derived from Streptomyces . Here, we report the enzymatic characteristics of the Ord1 and discuss its catalytic mechanism.


  • Organizational Affiliation
    • Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
prenyltransferase
A, B, C, D
337Streptomyces sp. KS84Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.254 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.879α = 93.455
b = 72.425β = 110.501
c = 83.774γ = 90.085
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan17KK0141
Japan Society for the Promotion of Science (JSPS)Japan21K06036

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release