PDBsum entry 1p5e

Cell cycle

PDB id: 1p5e

Contents

Protein chains

297 a.a. *

258 a.a. *

Ligands

TBS ×2

Waters ×242

* Residue conservation analysis

PDB id:

1p5e

Name:

Cell cycle

Title:

The structure of phospho-cdk2/cyclin a in complex with the inhibitor 4,5,6,7-tetrabromobenzotriazole (tbs)

Structure:

Cell division protein kinase 2. Chain: a, c. Synonym: p33 protein kinase. Engineered: yes. Cyclin a2. Chain: b, d. Fragment: residues 175-432. Synonym: cyclin a. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cdk2. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: ccna2 or ccna or ccn1.

Biol. unit:

Dimer (from PQS)

Resolution:

2.22Å R-factor: 0.219 R-free: 0.257

Authors:

E.De Moliner,N.R.Brown,L.N.Johnson

Key ref:

E.De Moliner et al. (2003). Alternative binding modes of an inhibitor to two different kinases. Eur J Biochem, 270, 3174-3181. PubMed id: 12869192 DOI: 10.1046/j.1432-1033.2003.03697.x

Date:

26-Apr-03 Release date: 01-Jul-03

Protein chains

P24941  (CDK2_HUMAN) -  Cyclin-dependent kinase 2 from Homo sapiens

Seq: 298 a.a.

Struc: 297 a.a.*

Protein chains

P20248  (CCNA2_HUMAN) -  Cyclin-A2 from Homo sapiens

Seq: 432 a.a.

Struc: 258 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, C: E.C.2.7.11.22 - cyclin-dependent kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1046/j.1432-1033.2003.03697.x

Eur J Biochem 270:3174-3181 (2003)

PubMed id: 12869192

Alternative binding modes of an inhibitor to two different kinases.

E.De Moliner, N.R.Brown, L.N.Johnson.

ABSTRACT

Protein kinases are targets for therapeutic agents designed to intervene in signaling processes in the diseased state. Most kinase inhibitors are directed towards the conserved ATP binding site. Because the essential features of this site are conserved in all eukaryotic protein kinases, it is generally assumed that the same compound will bind in a similar manner to different protein kinases. The inhibitor 4,5,6,7-tetrabromobenzotriazole (TBB) is a selective inhibitor for the protein kinase CK2 (IC50 1.6 micro m) (Sarno et al. (2001) FEBS Letts.496, 44-48). Three other kinases [cyclin-dependent protein kinase 2 (CDK2), phosphorylase kinase and glycogen synthase kinase 3beta] exhibit approximately 10-fold weaker affinity for TBB than CK2. We report the crystal structure of TBB in complex with phospho-CDK2-cyclin A at 2.2 A resolution and compare the interactions with those observed for TBB bound to CK2. TBB binds at the ATP binding site of both kinases. In CDK2, each of the four bromine atoms makes polar contacts either to main chain oxygens in the hinge region of the kinase or to water molecules, in addition to several van der Waals contacts. The mode of binding of TBB to CDK2 is different from that to CK2. TBB in CDK2 is displaced more towards the hinge region between the N- and C-terminal lobes and rotated relative to TBB in CK2. The ATP binding pocket is wider in CDK2 than in CK2 resulting in fewer van der Waals contacts but TBB in CK2 does not contact the hinge. The structures show that, despite the conservation of the ATP binding pocket, the inhibitor is able to exploit different recognition features so that the same compound can bind in different ways to the two different kinases.

Selected figure(s)

Figure 1.
Fig. 1. TBB binding to pCDK2–cyclin A.(A) Schematic representation of the structure of pCDK2 (yellow) and cyclin A (magenta) in complex with TBB (carbon atoms, green; nitrogen atoms, blue; and bromine atoms, cyan). TBB binds at the ATP binding site in the region between the N- and C-terminal lobes and makes contacts with residues in the hinge region. (B) Details of TBB fit to the final sigmaa weighted 2Fo-Fc electron density map. The map is contoured at levels corresponding to 1 (blue contours) and 4 (red contours). The position of ATP is shown superimposed (carbon atoms: black). These figures and those in Fig. 2 Go-were prepared with aesop (M. E. M. Noble, unpublished work).

Figure 2.
Fig. 2. Details of the interactions of TBB with pCDK2 and CK2. Polar contacts to the bromine atoms and hydrogen bonds from nitrogen atoms are shown as black dashed lines. (A) Stereo diagram of TBB bound to pCDK2 (pCDK2 carbon atoms are yellow, TBB carbon atoms are green, TBB bromine atoms are cyan). Ala144 is shown for reference although it does not make any van der Waals interactions with TBB. (B) Stereo diagram of TBB bound to CK2 (CK2 carbon atoms of residues in contact with TBB are orange, CK2 hinge region carbon atoms, which do not contact TBB, are white, TBB carbon atoms are dark green, TBB bromine atoms are magenta). (C) Superposition of TBB bound to pCDK2 (carbon atoms, green; bromine atoms, cyan) and TBB bound to CK2 (carbon atoms, dark green; bromine atoms, magenta). There is a shift of about 2.5 Å and a rotation of about 30° between the two TBB molecules.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2003, 270, 3174-3181) copyright 2003.