9FW6 | pdb_00009fw6

A ternary complex of plant adenosine kinase 1 from moss Physcomitrella patens (PpADK1) with adenosine and ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 
    0.255 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

A monomer-dimer switch modulates the activity of plant adenosine kinase.

Kopecny, D.J.Vigouroux, A.Belicek, J.Kopecna, M.Koncitikova, R.Friedecka, J.Mik, V.Supikova, K.Humplik, J.F.Le Berre, M.Plancqueel, S.Strnad, M.von Schwartzenberg, K.Novak, O.Morera, S.Kopecny, D.

(2025) J Exp Bot 

  • DOI: https://doi.org/10.1093/jxb/eraf094
  • Primary Citation of Related Structures:  
    8RF7, 8RGJ, 8RPA, 9FW6

  • PubMed Abstract: 

    Adenosine undergoes ATP-dependent phosphorylation catalyzed by adenosine kinase (ADK). In plants, ADK also phosphorylates cytokinin ribosides, transport forms of the hormone. Here, we investigated the substrate preferences, oligomeric states and structures of ADKs from moss (Physcomitrella patens) and maize (Zea mays) alongside metabolomic and phenotypic analyses. We showed that dexamethasone-inducible ZmADK overexpressor lines in Arabidopsis can benefit from a higher number of lateral roots and larger root areas under nitrogen starvation. We discovered that maize and moss enzymes can form dimers upon increasing protein concentration, setting them apart from the monomeric human and protozoal ADKs. Structural and kinetic analyses revealed a catalytically inactive unique dimer. Within the dimer, both active sites are mutually blocked. The activity of moss ADKs, exhibiting a higher propensity to dimerize, was tenfold lower compared to maize ADKs. Two monomeric structures in a ternary complex highlight the characteristic transition from an open to a closed state upon substrate binding. This suggests that the oligomeric state switch can modulate the activity of moss ADKs and likely other plant ADKs. Moreover, dimer association represents a novel negative feedback mechanism, helping to maintain steady levels of adenosine and AMP.


  • Organizational Affiliation

    Department of Experimental Biology, Faculty of Science, Palacký University, Olomouc CZ-78371, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosine kinase
A, B
361Physcomitrium patensMutation(s): 0 
Gene Names: ADKPHYPADRAFT_184505
EC: 2.7.1.20
UniProt
Find proteins for O49923 (Physcomitrium patens)
Explore O49923 
Go to UniProtKB:  O49923
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO49923
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ADN (Subject of Investigation/LOI)
Query on ADN

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free:  0.255 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.59α = 90
b = 93.083β = 90
c = 131.671γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech Republic21-07661S
Palacky University in OlomoucCzech RepublicIGA_PrF_2023_012
Agence Nationale de la Recherche (ANR)FranceANR-11-IDEX-0003

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release