6ZJB

Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor Gp5A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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Literature

Structural Basis for GTP versus ATP Selectivity in the NMP Kinase AK3.

Rogne, P.Dulko-Smith, B.Goodman, J.Rosselin, M.Grundstrom, C.Hedberg, C.Nam, K.Sauer-Eriksson, A.E.Wolf-Watz, M.

(2020) Biochemistry 59: 3570-3581

  • DOI: https://doi.org/10.1021/acs.biochem.0c00549
  • Primary Citation of Related Structures:  
    6ZJB, 6ZJD, 6ZJE

  • PubMed Abstract: 

    ATP and GTP are exceptionally important molecules in biology with multiple, and often discrete, functions. Therefore, enzymes that bind to either of them must develop robust mechanisms to selectively utilize one or the other. Here, this specific problem is addressed by molecular studies of the human NMP kinase AK3, which uses GTP to phosphorylate AMP. AK3 plays an important role in the citric acid cycle, where it is responsible for GTP/GDP recycling. By combining a structural biology approach with functional experiments, we present a comprehensive structural and mechanistic understanding of the enzyme. We discovered that AK3 functions by recruitment of GTP to the active site, while ATP is rejected and nonproductively bound to the AMP binding site. Consequently, ATP acts as an inhibitor with respect to GTP and AMP. The overall features with specific recognition of the correct substrate and nonproductive binding by the incorrect substrate bear a strong similarity to previous findings for the ATP specific NMP kinase adenylate kinase. Taken together, we are now able to provide the fundamental principles for GTP and ATP selectivity in the large NMP kinase family. As a side-result originating from nonlinearity of chemical shifts in GTP and ATP titrations, we find that protein surfaces offer a general and weak binding affinity for both GTP and ATP. These nonspecific interactions likely act to lower the available intracellular GTP and ATP concentrations and may have driven evolution of the Michaelis constants of NMP kinases accordingly.


  • Organizational Affiliation

    Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP:AMP phosphotransferase AK3, mitochondrial
A, B, C, D, E
227Homo sapiensMutation(s): 0 
Gene Names: AK3AK3L1AK6AKL3L
EC: 2.7.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIJ7 (Homo sapiens)
Explore Q9UIJ7 
Go to UniProtKB:  Q9UIJ7
PHAROS:  Q9UIJ7
GTEx:  ENSG00000147853 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UIJ7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G5P (Subject of Investigation/LOI)
Query on G5P

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
P1-(5'-ADENOSYL)-P5-(5'-GUANOSYL) PENTAPHOSPHATE
C20 H29 N10 O23 P5
CNMILLPGDWDFCZ-INFSMZHSSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.468α = 93.79
b = 66.76β = 93.95
c = 105.909γ = 89.71
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted G5PClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description