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Structural insight into nucleotide recognition by human death-associated protein kinase.

McNamara LK, Watterson DM, Brunzelle JS - Acta Crystallogr. D Biol. Crystallogr. (2009)

Bottom Line: Death-associated protein kinase (DAPK) is a member of the Ca(2+)/calmodulin-regulated family of serine/threonine protein kinases.The structure of DAPK-ADP-Mg(2+) was compared with a newly determined DAPK-AMP-PNP-Mg(2+) structure and the previously determined apo DAPK structure (PDB code 1jks).The comparison shows that nucleotide-induced changes are localized to the glycine-rich loop region of DAPK.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Drug Discovery and Chemical Biology, Northwestern University, Chicago, Illinois 60611, USA.

ABSTRACT
Death-associated protein kinase (DAPK) is a member of the Ca(2+)/calmodulin-regulated family of serine/threonine protein kinases. The role of the kinase activity of DAPK in eukaryotic cell apoptosis and the ability of bioavailable DAPK inhibitors to rescue neuronal death after brain injury have made it a drug-discovery target for neurodegenerative disorders. In order to understand the recognition of nucleotides by DAPK and to gain insight into DAPK catalysis, the crystal structure of human DAPK was solved in complex with ADP and Mg(2+) at 1.85 A resolution. ADP is a product of the kinase reaction and product release is considered to be the rate-limiting step of protein kinase catalytic cycles. The structure of DAPK-ADP-Mg(2+) was compared with a newly determined DAPK-AMP-PNP-Mg(2+) structure and the previously determined apo DAPK structure (PDB code 1jks). The comparison shows that nucleotide-induced changes are localized to the glycine-rich loop region of DAPK.

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Superposition by least-squares fitting of DAPK–ADP–Mg2+ and apo DAPK reveals little change between the two structures apart from in two key areas: the hinge region near Ala97 and the glycine-rich loop near Ser21. The DAPK–ADP–Mg2+ structure is shown in red and the apo DAPK structure is shown in beige. Protein residues from the N-terminal domain and hinge region are shown.
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fig2: Superposition by least-squares fitting of DAPK–ADP–Mg2+ and apo DAPK reveals little change between the two structures apart from in two key areas: the hinge region near Ala97 and the glycine-rich loop near Ser21. The DAPK–ADP–Mg2+ structure is shown in red and the apo DAPK structure is shown in beige. Protein residues from the N-terminal domain and hinge region are shown.

Mentions: A superposition of DAPK–ADP–Mg2+ and apo DAPK (PDB code 1jks; Tereshko et al., 2001 ▶) was calculated by least-squares fitting (Emsley & Cowtan, 2004 ▶) over all atoms and an r.m.s. deviation of 0.69 Å was obtained. Overall, the structures of DAPK–ADP–Mg2+ and apo DAPK are mostly superim­posable, except for localized differences in the hinge and glycine-rich loop regions. The hinge region has a slight change in positioning that starts at the Cα atom of Val96 and continues through residue Ala97. In the superposition, the Cα atom of Ala97 in the DAPK–ADP–Mg2+ complex (PDB code 3f5g) differs by 0.85 Å from the position of this atom in the apo DAPK structure (Fig. 2 ▶). The deviation in the glycine-rich loop of the DAPK structures begins at the Cα atom of Glu17 and continues through Phe24. The structure around Ser21 and Gly22 in DAPK–ADP–Mg2+ is apparently shifted towards the C-­terminal domain, resulting in a slight closing of the loop compared with the apo DAPK structure (Fig. 2 ▶). The amide N atom of Ser21 in the DAPK–ADP–Mg2+ structure differs by 1.10 Å from its position in the apo DAPK structure. The highly conserved Gly22 can be modeled in two conformations; the amide N of conformation A shown in Fig. 2 ▶ differs by 0.93 Å from the apo DAPK structure, while the amide N of conformation B (not shown in the figure) differs by 0.74 Å from the amide N of the apo DAPK structure.


Structural insight into nucleotide recognition by human death-associated protein kinase.

McNamara LK, Watterson DM, Brunzelle JS - Acta Crystallogr. D Biol. Crystallogr. (2009)

Superposition by least-squares fitting of DAPK–ADP–Mg2+ and apo DAPK reveals little change between the two structures apart from in two key areas: the hinge region near Ala97 and the glycine-rich loop near Ser21. The DAPK–ADP–Mg2+ structure is shown in red and the apo DAPK structure is shown in beige. Protein residues from the N-terminal domain and hinge region are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651756&req=5

fig2: Superposition by least-squares fitting of DAPK–ADP–Mg2+ and apo DAPK reveals little change between the two structures apart from in two key areas: the hinge region near Ala97 and the glycine-rich loop near Ser21. The DAPK–ADP–Mg2+ structure is shown in red and the apo DAPK structure is shown in beige. Protein residues from the N-terminal domain and hinge region are shown.
Mentions: A superposition of DAPK–ADP–Mg2+ and apo DAPK (PDB code 1jks; Tereshko et al., 2001 ▶) was calculated by least-squares fitting (Emsley & Cowtan, 2004 ▶) over all atoms and an r.m.s. deviation of 0.69 Å was obtained. Overall, the structures of DAPK–ADP–Mg2+ and apo DAPK are mostly superim­posable, except for localized differences in the hinge and glycine-rich loop regions. The hinge region has a slight change in positioning that starts at the Cα atom of Val96 and continues through residue Ala97. In the superposition, the Cα atom of Ala97 in the DAPK–ADP–Mg2+ complex (PDB code 3f5g) differs by 0.85 Å from the position of this atom in the apo DAPK structure (Fig. 2 ▶). The deviation in the glycine-rich loop of the DAPK structures begins at the Cα atom of Glu17 and continues through Phe24. The structure around Ser21 and Gly22 in DAPK–ADP–Mg2+ is apparently shifted towards the C-­terminal domain, resulting in a slight closing of the loop compared with the apo DAPK structure (Fig. 2 ▶). The amide N atom of Ser21 in the DAPK–ADP–Mg2+ structure differs by 1.10 Å from its position in the apo DAPK structure. The highly conserved Gly22 can be modeled in two conformations; the amide N of conformation A shown in Fig. 2 ▶ differs by 0.93 Å from the apo DAPK structure, while the amide N of conformation B (not shown in the figure) differs by 0.74 Å from the amide N of the apo DAPK structure.

Bottom Line: Death-associated protein kinase (DAPK) is a member of the Ca(2+)/calmodulin-regulated family of serine/threonine protein kinases.The structure of DAPK-ADP-Mg(2+) was compared with a newly determined DAPK-AMP-PNP-Mg(2+) structure and the previously determined apo DAPK structure (PDB code 1jks).The comparison shows that nucleotide-induced changes are localized to the glycine-rich loop region of DAPK.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Drug Discovery and Chemical Biology, Northwestern University, Chicago, Illinois 60611, USA.

ABSTRACT
Death-associated protein kinase (DAPK) is a member of the Ca(2+)/calmodulin-regulated family of serine/threonine protein kinases. The role of the kinase activity of DAPK in eukaryotic cell apoptosis and the ability of bioavailable DAPK inhibitors to rescue neuronal death after brain injury have made it a drug-discovery target for neurodegenerative disorders. In order to understand the recognition of nucleotides by DAPK and to gain insight into DAPK catalysis, the crystal structure of human DAPK was solved in complex with ADP and Mg(2+) at 1.85 A resolution. ADP is a product of the kinase reaction and product release is considered to be the rate-limiting step of protein kinase catalytic cycles. The structure of DAPK-ADP-Mg(2+) was compared with a newly determined DAPK-AMP-PNP-Mg(2+) structure and the previously determined apo DAPK structure (PDB code 1jks). The comparison shows that nucleotide-induced changes are localized to the glycine-rich loop region of DAPK.

Show MeSH
Related in: MedlinePlus