8RF7 | pdb_00008rf7

Crystal structure of maize adenosine kinase 2 (ADK2) apoform

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

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.262 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 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 

  • 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
360Zea 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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.262 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.222α = 90
b = 136.222β = 90
c = 78.226γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
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
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicCZ.02.01.01/00/22_008/0004581

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