5YSQ

Sulfate-complex structure of a pyrophosphate-dependent kinase in the ribokinase family provides insight into the donor-binding mode


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants.

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

(2018) Nat Commun 9: 1765-1765

  • DOI: https://doi.org/10.1038/s41467-018-04201-z
  • Primary Citation of Related Structures:  
    5YSP, 5YSQ

  • PubMed Abstract: 

    Almost all kinases utilize ATP as their phosphate donor, while a few kinases utilize pyrophosphate (PPi) instead. PPi-dependent kinases are often homologous to their ATP-dependent counterparts, but determinants of their different donor specificities remain unclear. We identify a PPi-dependent member of the ribokinase family, which differs from known PPi-dependent kinases, and elucidate its PPi-binding mode based on the crystal structures. Structural comparison and sequence alignment reveal five important residues: three basic residues specifically recognizing PPi and two large hydrophobic residues occluding a part of the ATP-binding pocket. Two of the three basic residues adapt a conserved motif of the ribokinase family for the PPi binding. Using these five key residues as a signature pattern, we discover additional PPi-specific members of the ribokinase family, and thus conclude that these residues are the determinants of PPi-specific binding. Introduction of these residues may enable transformation of ATP-dependent ribokinase family members into PPi-dependent enzymes.


  • 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
TM0415
A, B
286Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: TM_0415
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: 1.47 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.745α = 90
b = 62.354β = 103.97
c = 87.979γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan16J08482
Japan Society for the Promotion of ScienceJapan17H05439

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description