8RPA | pdb_00008rpa

Crystal structure of Zea mays adenosine kinase 3 (ZmADK3) in complex with AP5A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 
    0.257 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.210 (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 kinase361Zea maysMutation(s): 0 
Gene Names: 103646212ZEAMMB73_Zm00001d003017
EC: 2.7.1.20
UniProt
Find proteins for A0A1D6E5Z5 (Zea mays)
Explore A0A1D6E5Z5 
Go to UniProtKB:  A0A1D6E5Z5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D6E5Z5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AP5 (Subject of Investigation/LOI)
Query on AP5

Download Ideal Coordinates CCD File 
B [auth A]BIS(ADENOSINE)-5'-PENTAPHOSPHATE
C20 H29 N10 O22 P5
OIMACDRJUANHTJ-XPWFQUROSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free:  0.257 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.049α = 90
b = 117.49β = 90
c = 165.958γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
Aimlessdata scaling
autoPROCdata processing
BUSTERrefinement
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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)FranceJean d'Alembert fellowship as part of France 2030 program ANR-11-IDEX-0003

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references
  • Version 1.2: 2025-09-03
    Changes: Database references