PDBsum entry 2w96

Cell cycle

PDB id: 2w96

Contents

Protein chains

249 a.a. *

267 a.a. *

Ligands

GOL

Waters ×190

* Residue conservation analysis

PDB id:

2w96

Name:

Cell cycle

Title:

Crystal structure of cdk4 in complex with a d-type cyclin

Structure:

G1/s-specific cyclin-d1. Chain: a. Synonym: d-type cyclin, prad1 oncogene. Engineered: yes. Cell division protein kinase 4. Chain: b. Fragment: kinase domain, residues 1-44,48-303. Synonym: cdk4, cyclin-dependent kinase 4, psk-j3. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf21.

Resolution:

2.30Å R-factor: 0.205 R-free: 0.259

Authors:

P.J.Day,A.Cleasby,I.J.Tickle,M.O.Reilly,J.E.Coyle,F.P.Holding, R.L.Mcmenamin,J.Yon,R.Chopra,C.Lengauer,H.Jhoti

Key ref:

P.J.Day et al. (2009). Crystal structure of human CDK4 in complex with a D-type cyclin. Proc Natl Acad Sci U S A, 106, 4166-4170. PubMed id: 19237565 DOI: 10.1073/pnas.0809645106

Date:

21-Jan-09 Release date: 10-Mar-09

Protein chain

P24385  (CCND1_HUMAN) -  G1/S-specific cyclin-D1 from Homo sapiens

Seq: 295 a.a.

Struc: 249 a.a.

Protein chain

P11802  (CDK4_HUMAN) -  Cyclin-dependent kinase 4 from Homo sapiens

Seq: 303 a.a.

Struc: 267 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chain B: 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: 10.1073/pnas.0809645106

Proc Natl Acad Sci U S A 106:4166-4170 (2009)

PubMed id: 19237565

Crystal structure of human CDK4 in complex with a D-type cyclin.

P.J.Day, A.Cleasby, I.J.Tickle, M.O'Reilly, J.E.Coyle, F.P.Holding, R.L.McMenamin, J.Yon, R.Chopra, C.Lengauer, H.Jhoti.

ABSTRACT

The cyclin D1-cyclin-dependent kinase 4 (CDK4) complex is a key regulator of the transition through the G(1) phase of the cell cycle. Among the cyclin/CDKs, CDK4 and cyclin D1 are the most frequently activated by somatic genetic alterations in multiple tumor types. Thus, aberrant regulation of the CDK4/cyclin D1 pathway plays an essential role in oncogenesis; hence, CDK4 is a genetically validated therapeutic target. Although X-ray crystallographic structures have been determined for various CDK/cyclin complexes, CDK4/cyclin D1 has remained highly refractory to structure determination. Here, we report the crystal structure of CDK4 in complex with cyclin D1 at a resolution of 2.3 A. Although CDK4 is bound to cyclin D1 and has a phosphorylated T-loop, CDK4 is in an inactive conformation and the conformation of the heterodimer diverges from the previously known CDK/cyclin binary complexes, which suggests a unique mechanism for the process of CDK4 regulation and activation.

Selected figure(s)

Figure 1.
Ribbon diagram of the CDK4 (cyan)/cyclin D1 (orange) heterodimer. (A) The N- and C-terminal lobes of the kinase are labeled as are key secondary structural elements. (B) CDK7 (yellow) (Protein Data Bank ID code 1UA2) and CDK4 (cyan) (rmsd 1.053 Å). Both the αC-helix and T-loop of CDK7 adopt inactive conformations that are similar to the conformations of the equivalent secondary structural elements observed in CDK4.

Figure 3.
Architecture of the engineered loop preceding the αC-helix in the CDK4 (cyan)/cyclin D1 (orange) structure. (A) Akin to CDK2 and CDK6 (see Fig. S4) the apex of the loop is stabilized by hydrogen bonds from the loop main chain to a highly-conserved lysine (Lys[D1]112) and glutamate (Glu[D1]141) on the cyclin. The second glutamate (Glu[K4]44′) from the GE′E′G insertion mimics the interactions formed by the glutamate in the CDK6 structure. The loop is further stabilized by intramolecular H-bonds, which are not observed in either the CDK2 or CDK6 structures. A cyclin D1 Lys[D1]112–Glu mutation results in aberrant CDK4/cyclin D1 complex assembly and activation. (B) Residues in the vicinity of cyclin D1 (orange) Lys[D1]114. The Lys[D1]114–Glu mutation results in defective CDK4/cyclin D1 complex formation. Lys[D1]114 sits within an acidic environment formed by Glu[D1]74, Glu[D1]75, Glu[D1]76, Asp[D1]159, and Glu[D1]162. It would be anticipated that introduction of an additional negative charge into this environment would be highly destabilizing and significantly perturb correct CDK/cyclin association.

Figures were selected by an automated process.