Primary Citation PubMed: 14529625
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Structural insight into nucleotide recognition by human death-associated protein kinase.
(2009) Acta Crystallogr D Biol Crystallogr 65
PubMed: 19237746 | PubMedCentral: PMC2651756 | DOI: 10.1107/S0907444908043679
For example, observation of negative density or a lack of density corresponding to the γ-phosphate of AMP-PNP in a kinase complex can be seen in the electron-density maps of structure... such as GSK3β–AMP-PNP (PDB code 1pyx ), Polo-like kinase 1 (PDB code 2ou7 ), CK2–AMP-PNP ( 1lp4 ), Pim 1 kinase–AMP-PNP (PDB code 1yxt ) and serum/glucocorticoid regulated kinase–AMP-PNP (PDB code 2r5t ).
Publication Year: 2009
Allosteric regulation of glycogen synthase kinase 3?: a theoretical study.
(2010) Biochemistry 49
PubMed: 21105670 | PubMedCentral: PMC3005830 | DOI: 10.1021/bi100822q
(a) The final simulation snapshot of GSK-3β(p)·ATP (colored blue) superimposed on the crystal structure of PDB code 1PYX (colored red) from which the simulation originated.
The structure of the unphosphorylated inactive unbound enzyme with ATP (apo GSK-3β·ATP) was derived from PDB code 1PYX ( 6 ), and the existing ATP analogue, ANP, was replaced by ATP using CHARMM ( 36 ).
(b) The final simulation snapshot of GSK-3β·ATP (colored blue) superimposed on the crystal structure of PDB code 1PYX (colored red) from which the simulation originated.
Publication Year: 2010
Structural basis of GSK-3 inhibition by N-terminal phosphorylation and by the Wnt receptor LRP6.
(2014) Elife 3
PubMed: 24642411 | PubMedCentral: PMC3953950 | DOI: 10.7554/eLife.01998
In the inhibitor-free structure ( Figure 2C ), these basic residues form hydrogen bonds with a molecule of glycerol present in the phosphate-binding site, and a previous structure of GSK-3 bound to a ... on-hydrolyzable ATP analog AMP-PNP shows that water molecules occupy this site (PDB 1PYX; Bertrand et al., 2003 ).
Some GSK-3 structures show an intermediate position of the glycine-rich loop (green/pink) due to interaction with another GSK-3 molecule in the crystal lattice (not shown in the figure for clarity, please refer to PDB 1H8F/1PYX).
For example, Phe67 is found in several positions in peptide inhibitor-free GSK-3 structures, and some of them (e.g., PDB 1PYX) would clash with the C-loop in the peptide-bound structures ( Figure 4A ).
Publication Year: 2014
PubMed ID is not available.
Published in 2015
These structures include pCDK2/cyclin A/ADP/2MG/MgF 3 - /peptide complex (PDB code 3QHR [ 21 ]), GSK3β/AMP-PNP/2MG complex (PDB code 1PYX [ 30 ]), MST3/ADP/2MN complex (PDB code 3A7J [ 48 ]), ... KAc/AMP-PCP/2MG complex (PDB code 4IAC [ 49 ]), PKB/AMP-PNP/2MN complex (PDB code 1O6L [ 50 ]) and p38γ/AMP-PNP/2MG complex(PDB code 1CM8 [ 51 ]) ( S2 Table ).
(A) pCDK2/cyclin A/ADP/2MG/MgF 3 - /peptide complex (PDB code 3QHR), (B) GSK3β/AMP-PNP/2MG complex (PDB code 1PYX), (C) MST3/ADP/2MN complex (PDB code 3A7J), (D) PKAc/AMP-PCP/2MG complex (PDB code 4IAC), (E) PKB/AMP-PNP/2MN complex (PDB code 1O6L), (F) p38γ/AMP-PNP/2MG complex (PDB code 1CM8).
The missing Mg 2+ ion at site 1 (Mg 1 2+ ion) was modeled into its position by aligning the crystal structure of GSK3β in the complex with ATP analog adenosine 5′-(β,γ-imidotriphosphate) (AMP-PNP) and two Mg 2+ ions (PDB code 1PYX) [ 30 ] with the pCDK9/cyclin T1/ATP/1MG complex crystal structure.
Publication Year: 2015
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