ISDA

Deposition Date 2002-05-08

Release Date 2002-05-29

Last Version Date 2023-10-25

Entry Detail

PDB ID:

1LPU

Keywords:

TRANSFERASE

Title:

Low Temperature Crystal Structure of the Apo-form of the catalytic subunit of protein kinase CK2 from Zea mays

Biological Source:

Source Organism:

Zea mays (Taxon ID: 4577)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.86 Å

R-Value Free:

0.24

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

C 1 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Protein kinase CK2
Gene (Uniprot):ACK2
Chain IDs:A
Chain Length:332
Number of Molecules:1
Biological Source:Zea mays

UniProt ID:P28523 Pfam ID:PF00069 EC:2.7.11.1

Ligand Molecules

BEN

Primary Citation

Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate.

Yde, C.W, Ermakova, I, Issinger, O.G, Niefind, K, Niefind, K, Guerra, B, Pinna, L.A, Issinger, O.-G, Schomburg, D, Guerra, B, Niefind, K, Pinna, L.A, Schomburg, D, Issinger, O.-G, Niefind, K, Putter, M, Guerra, B, Issinger, O.-G, Schomburg, D, Niefind, K, Guerra, B, Ermakowa, I, Issinger, O.-G, Niefind, K, Guerra, B, Ermakowa, I, Issinger, O.-G, Boldyreff, B, Meggio, F, Dobrowolska, G, Pinna, L.A, Issinger, O.-G, Dobrowolska, G, Boldyreff, B, Issinger, O.-G.Show

J.Mol.Biol. 347 399 414 (2005)

PMID: 15740749 DOI: 10.1016/j.jmb.2005.01.003

Abstact

Protein kinase CK2 (casein kinase 2) is a highly conserved and ubiquitously found eukaryotic serine/threonine kinase that plays a role in various cellular key processes like proliferation, apoptosis and circadian rhythm. One of its prominent biochemical properties is its ability to use GTP as well as ATP as a cosubstrate (dual-cosubstrate specificity). This feature is exceptional among eukaryotic protein kinases, and its biological significance is unknown. We describe here a mutant of the catalytic subunit of protein kinase CK2 (CK2alpha) from Homo sapiens (hsCK2alpha) with a clear and CK2-atypical preference for ATP compared to GTP. This mutant was designed on the basis of several structures of CK2alpha from Zea mays (zmCK2alpha) in complex with various ATP-competitive ligands. A structural overlay revealed the existence of a "purine base binding plane" harbouring the planar moiety of the respective ligand like the purine base of ATP and GTP. This purine base binding plane is sandwiched between the side-chains of Ile66 (Val66 in hsCK2alpha) and Met163, and it adopts a significantly different orientation than in prominent homologues like cAMP-dependent protein kinase (CAPK). By exchanging these two flanking amino acids (Val66Ala, Met163Leu) in hsCK2alpha(1-335), a C-terminally truncated variant of hsCK2alpha, the cosubstrate specificity shifted in the expected direction so that the mutant strongly favours ATP. A structure determination of the mutant in complex with an ATP-analogue confirmed the predicted change of the purine base binding plane orientation. An unexpected but in retrospect plausible consequence of the mutagenesis was, that the helix alpha D region, which is in the direct neighbourhood of the ATP-binding site, has adopted a conformation that is more similar to CAPK and less favourable for binding of GTP. These findings demonstrate that CK2alpha possesses sophisticated structural adaptations in favour of dual-cosubstrate specificity, suggesting that this property could be of biological significance.

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