8RGJ | pdb_00008rgj

Structure of maize adenosine kinase 2 (ADK2) in complex with AMP-PCP

  • Classification: TRANSFERASE
  • Organism(s): Zea mays
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-12-13 Released: 2025-01-01 
  • Deposition Author(s): Morera, S., Kopecny, D., Vigouroux, A.
  • Funding Organization(s): Palacky University in Olomouc, Agence Nationale de la Recherche (ANR), Ministry of Education, Youth and Sports of the Czech Republic, Czech Science Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 
    0.278 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.260 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.261 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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 76: 3457-3479

  • 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 kinase360Zea maysMutation(s): 0 
Gene Names: ZEAMMB73_Zm00001d017271
EC: 2.7.1.20
UniProt
Find proteins for B4FFH8 (Zea mays)
Explore B4FFH8 
Go to UniProtKB:  B4FFH8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4FFH8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosine kinase360Zea maysMutation(s): 0 
Gene Names: ZEAMMB73_Zm00001d017271
EC: 2.7.1.20
UniProt
Find proteins for B4FFH8 (Zea mays)
Explore B4FFH8 
Go to UniProtKB:  B4FFH8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4FFH8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free:  0.278 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.260 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.261 (Depositor) 
Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.85α = 90
b = 135.85β = 90
c = 78.634γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
autoPROCdata processing
Aimlessdata scaling
autoPROCdata processing
BUSTERrefinement
autoPROCdata reduction
FFTphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Palacky University in OlomoucCzech RepublicIGA_PrF_2023_012
Agence Nationale de la Recherche (ANR)FranceANR-11-IDEX-0003
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicCZ.02.01.01/00/22_008/0004581
Czech Science FoundationCzech Republic21-07661S

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references
  • Version 1.2: 2025-09-03
    Changes: Database references