7E4L

Conversion of pyrophosphate-dependent myo-inositol-1 kinase into myo-inositol-3 kinase by N78L/S89L mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Altering the Phosphorylation Position of Pyrophosphate-Dependent myo -Inositol-1-Kinase Based on Its Crystal Structure.

Tashiro, R.Sato, T.Atomi, H.Miki, K.Fujihashi, M.

(2021) ACS Chem Biol 16: 794-799

  • DOI: https://doi.org/10.1021/acschembio.0c00733
  • Primary Citation of Related Structures:  
    7E4L

  • PubMed Abstract: 

    Most kinases utilize ATP as a phosphate donor and phosphorylate a wide range of phosphate acceptors. An alternative phosphate donor is inorganic pyrophosphate (PPi), which costs only 1/1000 of ATP. To develop a method to engineer PPi-dependent kinases, we herein aimed to alter the product of PPi-dependent myo -inositol kinase from d- myo- inositol 1-phosphate to d- myo- inositol 3-phosphate. For this purpose, we introduced the myo- inositol recognition residues of the ATP-dependent myo- inositol-3-kinase into the PPi-dependent myo -inositol-1-kinase. This replacement was expected to change the 3D arrangements of myo -inositol in the active site and bring the hydroxyl group at the 3C position close to the catalytic residue. LC-MS and NMR analyses proved that the engineered enzyme successfully produced myo- inositol 3-phosphate from PPi and myo- inositol.


  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PfkB domain-containing protein
A, B
286Thermotoga maritima MSB8Mutation(s): 2 
Gene Names: Tmari_0412
UniProt
Find proteins for Q9WYP6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WYP6 
Go to UniProtKB:  Q9WYP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WYP6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.205α = 83.53
b = 46.398β = 80.43
c = 66.544γ = 68.57
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

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)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-06-02
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description