9V4H | pdb_00009v4h

Prenyltransferase Ord1 Q216A-FSPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.253 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 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 64: 4196-4205

  • DOI: https://doi.org/10.1021/acs.biochem.5c00329
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 145.37 kDa 
  • Atom Count: 8,450 
  • Modeled Residue Count: 1,121 
  • Deposited Residue Count: 1,348 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
prenyltransferase
A, B, C, D
337Streptomyces sp. KS84Mutation(s): 0 
UniProt
Find proteins for A0A0F7CMZ4 (Streptomyces xiamenensis)
Explore A0A0F7CMZ4 
Go to UniProtKB:  A0A0F7CMZ4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F7CMZ4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.253 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.93α = 86.28
b = 71.87β = 69.39
c = 84γ = 89.99
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 1.1: 2025-10-22
    Changes: Database references