Limits...
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.

Show MeSH

Related in: MedlinePlus

DAPK–nucleotide–Mg2+ interactions. (a) ADP–Mg2+ interactions with DAPK. (b) AMP-PNP–Mg2+ interactions with DAPK.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2651756&req=5

fig4: DAPK–nucleotide–Mg2+ interactions. (a) ADP–Mg2+ interactions with DAPK. (b) AMP-PNP–Mg2+ interactions with DAPK.

Mentions: The determination of a DAPK–ADP–Mg2+ structure and a DAPK–AMP-PNP–Mg2+ structure with sufficient density to allow placement of the β- and γ-phosphates facilitated a comparison of the two protein conformations and examination of the bound nucleotides in the two DAPK structures. Superposition of DAPK–AMP-PNP–Mg2+ and DAPK–ADP–Mg2+ by a least-squares fit over all atoms revealed an r.m.s. deviation of 0.67 Å between the two structures. Examination of the details of nucleotide interactions in the DAPK–ADP–Mg2+ and DAPK–AMP-PNP–Mg2+ structures re­vealed con­servation of some key distances between the protein and the adenine and ribose portions of the nucleotides (Figs. 4 ▶ a and 4 ▶ b). For example, the adenine bases of AMP-PNP and ADP make conserved contacts with the hinge region of the kinase. The N1 atoms of the adenine rings are both 3.1 Å from the amide N atom of Val96. The N6 atom of the adenine ring is 2.7 Å away from the carboxyl of Glu94. The ribose-ring O2* and O3* atoms make conserved interactions with Glu100 in the ADP and AMP-PNP structures.


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

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

DAPK–nucleotide–Mg2+ interactions. (a) ADP–Mg2+ interactions with DAPK. (b) AMP-PNP–Mg2+ interactions with DAPK.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig4: DAPK–nucleotide–Mg2+ interactions. (a) ADP–Mg2+ interactions with DAPK. (b) AMP-PNP–Mg2+ interactions with DAPK.
Mentions: The determination of a DAPK–ADP–Mg2+ structure and a DAPK–AMP-PNP–Mg2+ structure with sufficient density to allow placement of the β- and γ-phosphates facilitated a comparison of the two protein conformations and examination of the bound nucleotides in the two DAPK structures. Superposition of DAPK–AMP-PNP–Mg2+ and DAPK–ADP–Mg2+ by a least-squares fit over all atoms revealed an r.m.s. deviation of 0.67 Å between the two structures. Examination of the details of nucleotide interactions in the DAPK–ADP–Mg2+ and DAPK–AMP-PNP–Mg2+ structures re­vealed con­servation of some key distances between the protein and the adenine and ribose portions of the nucleotides (Figs. 4 ▶ a and 4 ▶ b). For example, the adenine bases of AMP-PNP and ADP make conserved contacts with the hinge region of the kinase. The N1 atoms of the adenine rings are both 3.1 Å from the amide N atom of Val96. The N6 atom of the adenine ring is 2.7 Å away from the carboxyl of Glu94. The ribose-ring O2* and O3* atoms make conserved interactions with Glu100 in the ADP and AMP-PNP structures.

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