PDBsum entry 4eok

Transferase/transferase inhibitor

PDB id: 4eok

Contents

Protein chains

294 a.a.

258 a.a.

Ligands

4SP ×2

SGM ×2

Waters ×8

PDB id:

4eok

Name:

Transferase/transferase inhibitor

Title:

Thr 160 phosphorylated cdk2 h84s, q85m, k89d - human cyclin a3 complex with the inhibitor nu6102

Structure:

Cyclin-dependent kinase 2. Chain: a, c. Synonym: cell division protein kinase 2, p33 protein kinase. Engineered: yes. Mutation: yes. Cyclin-a2. Chain: b, d. Fragment: c-terminal fragment. Synonym: cyclin-a.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cdk2, cdkn2. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: ccna2, ccn1, ccna. Expression_system_taxid: 562

Resolution:

2.57Å R-factor: 0.225 R-free: 0.259

Authors:

A.Echalier,E.Cot,A.Camasses,E.Hodimont,F.Hoh,F.Sheinerman, L.Krasinska,D.Fisher

Key ref:

A.Echalier et al. (2012). An integrated chemical biology approach provides insight into Cdk2 functional redundancy and inhibitor sensitivity. Chem Biol, 19, 1028-1040. PubMed id: 22921070

Date:

14-Apr-12 Release date: 06-Feb-13

Protein chains

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

Seq: 298 a.a.

Struc: 294 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 4 residue positions (black crosses)

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

Chem Biol 19:1028-1040 (2012)

PubMed id: 22921070

An integrated chemical biology approach provides insight into Cdk2 functional redundancy and inhibitor sensitivity.

A.Echalier, E.Cot, A.Camasses, E.Hodimont, F.Hoh, P.Jay, F.Sheinerman, L.Krasinska, D.Fisher.

ABSTRACT

Cdk2 promotes DNA replication and is a promising cancer therapeutic target, but its functions appear redundant with Cdk1, an essential Cdk affected by most Cdk2 inhibitors. Here, we present an integrated multidisciplinary approach to address Cdk redundancy. Mathematical modeling of enzymology data predicted conditions allowing selective chemical Cdk2 inhibition. Together with experiments in Xenopus egg extracts, this supports a rate-limiting role for Cdk2 in DNA replication. To confirm this we designed inhibitor-resistant (ir)-Cdk2 mutants using a novel bioinformatics approach. Bypassing inhibition with ir-Cdk2 or with Cdk1 shows that Cdk2 is rate-limiting for replication in this system because Cdk1 is insufficiently active. Additionally, crystal structures and kinetics reveal alternative binding modes of Cdk1-selective and Cdk2-selective inhibitors and mechanisms of Cdk2 inhibitor resistance. Our approach thus provides insight into structure, functions, and biochemistry of a cyclin-dependent kinase.