7VMW

Crystal structure of LimF prenyltransferase bound with a peptide substrate and GSPP

• PDB DOI: https://doi.org/10.2210/pdb7VMW/pdb

• Classification: TRANSFERASE
• Organism(s): Limnothrix sp. CACIAM 69d, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-10-09 Released: 2022-08-03 
• Deposition Author(s): Hamada, K., Kobayashi, S., Okada, C., Zhang, Y., Inoue, S., Goto, Y., Suga, H., Ogata, K., Sengoku, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.232 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

LimF is a versatile prenyltransferase for histidine-C-geranylation on diverse non-natural substrates

Zhang, Y., Hamada, K., Nguyen, D.T., Inoue, S., Satake, M., Kobayashi, S., Okada, C., Ogata, K., Okada, M., Sengoku, T., Goto, Y., Suga, H.

(2022) Nat Catal 

• DOI: https://doi.org/10.1038/s41929-022-00822-2

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.53 kDa 
• Atom Count: 5,305 
• Modelled Residue Count: 597 
• Deposited Residue Count: 611 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LynF/TruF/PatF family peptide O-prenyltransferase	A, B	302	Limnothrix sp. CACIAM 69d	Mutation(s): 0  Gene Names: BJG00_018450
UniProt
Find proteins for A0A372DCN7 (Limnothrix sp. CACIAM 69d) Explore A0A372DCN7  Go to UniProtKB:  A0A372DCN7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
substrate peptide	C	7	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GST (Subject of Investigation/LOI)	E [auth A]	GERANYL S-THIOLODIPHOSPHATE C10 H20 O6 P2 S AKIXWSDUEPPMKM-JXMROGBWSA-N
PPV (Subject of Investigation/LOI)	G [auth B]	PYROPHOSPHATE H4 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.232 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.66	α = 90
b = 48.43	β = 117.869
c = 91.04	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-03 
Deposition Author(s): Hamada, K., Kobayashi, S., Okada, C., Zhang, Y., Inoue, S., Goto, Y., Suga, H., Ogata, K., Sengoku, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-08-03
  Type: Initial release
  
• Version 1.1: 2022-08-10
  Changes: Structure summary
• Version 1.2: 2022-08-24
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary