PDBsum entry: 1h25

Transferase

PDB id: 1h25

Contents

Protein chains

294 a.a. *

258 a.a. *

279 a.a. *

Ligands

PRO-LYS-PRO-LEU-LYS-LYS-LEU-ARG-PHE-ASP

Waters ×192

* Residue conservation analysis

PDB id:

1h25

Name:

Transferase

Title:

Cdk2/cyclin a in complex with an 11-residue recruitment peptide from retinoblastoma-associated protein

Structure:

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

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 9606

Biol. unit:

Dimer (from PDB file)

Resolution:

2.5Å R-factor: 0.249 R-free: 0.266

Authors:

I.Tews,K.Y.Cheng,E.D.Lowe,M.E.M.Noble,N.R.Brown,S.Gul, S.Gamblin,L.N.Johnson

Key ref:

E.D.Lowe et al. (2002). Specificity determinants of recruitment peptides bound to phospho-CDK2/cyclin A. Biochemistry, 41, 15625-15634. PubMed id: 12501191 DOI: 10.1021/bi0268910

Date:

31-Jul-02 Release date: 01-Feb-03

Protein chain

P24941  (CDK2_HUMAN) -  Cyclin-dependent kinase 2

Seq: 298 a.a.

Struc: 294 a.a.*

Protein chains

P20248  (CCNA2_HUMAN) -  Cyclin-A2

Seq: 432 a.a.

Struc: 258 a.a.

Protein chain

P24941  (CDK2_HUMAN) -  Cyclin-dependent kinase 2

Seq: 298 a.a.

Struc: 279 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, C: E.C.2.7.11.22 - Cyclin-dependent kinase.
• Reaction: ATP + a protein = ADP + a phosphoprotein

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cyclin-dependent protein kinase holoenzyme complex (15 terms)
• Biological process: regulation of gene silencing (34 terms)
• Biochemical function: nucleotide binding (13 terms)

reference

DOI no: 10.1021/bi0268910

Biochemistry 41:15625-15634 (2002)

PubMed id: 12501191

Specificity determinants of recruitment peptides bound to phospho-CDK2/cyclin A.

E.D.Lowe, I.Tews, K.Y.Cheng, N.R.Brown, S.Gul, M.E.Noble, S.J.Gamblin, L.N.Johnson.

ABSTRACT

Progression through S phase of the eukaryotic cell cycle is regulated by the action of the cyclin dependent protein kinase 2 (CDK2) in association with cyclin A. CDK2/cyclin A phosphorylates numerous substrates. Substrate specificity often employs a dual recognition strategy in which the sequence flanking the phospho-acceptor site (Ser.Pro.X.Arg/Lys) is recognized by CDK2, while the cyclin A component of the complex contains a hydrophobic site that binds Arg/Lys.X.Leu ("RXL" or "KXL") substrate recruitment motifs. To determine additional sequence specificity motifs around the RXL sequence, we have performed X-ray crystallographic studies at 2.3 A resolution and isothermal calorimetry measurements on complexes of phospho-CDK2/cyclin A with a recruitment peptide derived from E2F1 and with shorter 11-mer peptides from p53, pRb, p27, E2F1, and p107. The results show that the cyclin recruitment site accommodates a second hydrophobic residue either immediately C-terminal or next adjacent to the leucine of the "RXL" motif and that this site makes important contributions to the recruitment peptide recognition. The arginine of the RXL motif contacts a glutamate, Glu220, on the cyclin. In those substrates that contain a KXL motif, no ionic interactions are observed with the lysine. The sequences N-terminal to the "RXL" motif of the individual peptides show no conservation, but nevertheless make common contacts to the cyclin through main chain interactions. Thus, the recruitment site is able to recognize diverse but conformationally constrained target sequences. The observations have implications for the further identification of physiological substrates of CDK2/cyclin A and the design of specific inhibitors.