PDBsum entry: 2a2k

Hydrolase

PDB id: 2a2k

Contents

Protein chain

171 a.a. *

Ligands

SO4

Metals

_CL ×2

Waters ×219

* Residue conservation analysis

PDB id:

2a2k

Name:

Hydrolase

Title:

Crystal structure of an active site mutant, c473s, of cdc25b phosphatase catalytic domain

Structure:

M-phase inducer phosphatase 2. Chain: a. Fragment: catalytic domain. Synonym: dual specificity phosphatase cdc25b. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cdc25b, cdc25hu2. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

1.52Å R-factor: 0.182 R-free: 0.191

Authors:

J.Sohn,J.Parks,G.Buhrman,P.Brown,K.Kristjansdottir,A.Safi, W.Yang,H.Edelsbrunner,J.Rudolph

Key ref:

J.Sohn et al. (2005). Experimental Validation of the Docking Orientation of Cdc25 with Its Cdk2-CycA Protein Substrate. Biochemistry, 44, 16563-16573. PubMed id: 16342947 DOI: 10.1021/bi0516879

Date:

22-Jun-05 Release date: 03-Jan-06

Protein chain

P30305  (MPIP2_HUMAN) -  M-phase inducer phosphatase 2

Seq: 580 a.a.

Struc: 171 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.1.3.48 - Protein-tyrosine-phosphatase.
• Reaction: Protein tyrosine phosphate + H₂O = protein tyrosine + phosphate

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

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (1 term)
• Biological process: M phase of mitotic cell cycle (2 terms)
• Biochemical function: protein tyrosine phosphatase activity (1 term)

reference

DOI no: 10.1021/bi0516879

Biochemistry 44:16563-16573 (2005)

PubMed id: 16342947

Experimental Validation of the Docking Orientation of Cdc25 with Its Cdk2-CycA Protein Substrate.

J.Sohn, J.M.Parks, G.Buhrman, P.Brown, K.Kristjánsdóttir, A.Safi, H.Edelsbrunner, W.Yang, J.Rudolph.

ABSTRACT

Cdc25 phosphatases are key activators of the eukaryotic cell cycle and compelling anticancer targets because their overexpression has been associated with numerous cancers. However, drug discovery targeting these phosphatases has been hampered by the lack of structural information about how Cdc25s interact with their native protein substrates, the cyclin-dependent kinases. Herein, we predict a docked orientation for Cdc25B with its Cdk2-pTpY-CycA protein substrate by a rigid-body docking method and refine the docked models with full-scale molecular dynamics simulations and minimization. We validate the stable ensemble structure experimentally by a variety of in vitro and in vivo techniques. Specifically, we compare our model with a crystal structure of the substrate-trapping mutant of Cdc25B. We identify and validate in vivo a novel hot-spot residue on Cdc25B (Arg492) that plays a central role in protein substrate recognition. We identify a hot-spot residue on the substrate Cdk2 (Asp206) and confirm its interaction with hot-spot residues on Cdc25 using hot-spot swapping and double mutant cycles to derive interaction energies. Our experimentally validated model is consistent with previous studies of Cdk2 and its interaction partners and initiates the opportunity for drug discovery of inhibitors that target the remote binding sites of this protein-protein interaction.