9V4J | pdb_00009v4j

Prenyltransferase Ord1 Wild type-FSPP

PDB DOI: https://doi.org/10.2210/pdb9V4J/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces sp. KS84
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-05-23 Released: 2025-10-01
Deposition Author(s): Oshiro, T., Uehara, S., Ito, T., Tanaka, Y., Kodera, Y., Matsui, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.272 (Depositor), 0.272 (DCC)
R-Value Work:
0.238 (Depositor), 0.238 (DCC)
R-Value Observed:
0.241 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

PubMed: 40968638 Search on PubMed
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: 145.76 kDa
Atom Count: 8,345
Modeled Residue Count: 1,079
Deposited Residue Count: 1,348
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
prenyltransferase	A, B, C, D	337	Streptomyces sp. KS84	Mutation(s): 0
UniProt
Find proteins for A0A0F7CMZ4 (Streptomyces xiamenensis) Explore A0A0F7CMZ4 Go to UniProtKB: A0A0F7CMZ4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0F7CMZ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FPS Query on FPS Download:Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE C₁₅ H₂₈ O₆ P₂ S MYMLCRQRXFRQGP-YFVJMOTDSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], J [auth C], L [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain L [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D]	M [auth D], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain M [auth D] Focus chain N [auth D]