PDBsum entry: 1mkp

Hydrolase

PDB id: 1mkp

Contents

Protein chain

144 a.a. *

Ligands

MPD

Metals

_CL

Waters ×40

* Residue conservation analysis

PDB id:

1mkp

Name:

Hydrolase

Title:

Crystal structure of pyst1 (mkp3)

Structure:

Pyst1. Chain: a. Fragment: catalytic domain. Synonym: dual specificity phosphatase, map kinase phosphatase 3, mkp-3. Engineered: yes. Mutation: yes. Other_details: mpd and chloride ion

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.35Å R-factor: 0.201 R-free: 0.235

Authors:

A.E.Stewart,S.Dowd,S.Keyse,N.Q.Mcdonald

Key ref:

A.E.Stewart et al. (1999). Crystal structure of the MAPK phosphatase Pyst1 catalytic domain and implications for regulated activation. Nat Struct Biol, 6, 174-181. PubMed id: 10048930 DOI: 10.1038/5861

Date:

11-Jul-98 Release date: 22-Jul-99

Protein chain

Q16828  (DUS6_HUMAN) -  Dual specificity protein phosphatase 6

Seq: 381 a.a.

Struc: 144 a.a.*

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

Enzyme reactions

• Enzyme class 1: E.C.3.1.3.16 - Phosphoprotein phosphatase.
• Reaction: A phosphoprotein + H₂O = a protein + phosphate
• Enzyme class 2: E.C.3.1.3.48 - Protein-tyrosine-phosphatase.
• Reaction: Protein tyrosine phosphate + H₂O = protein tyrosine + phosphate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

 Gene Ontology (GO) functional annotation 

• Biological process: dephosphorylation (2 terms)
• Biochemical function: phosphatase activity (3 terms)

reference

DOI no: 10.1038/5861

Nat Struct Biol 6:174-181 (1999)

PubMed id: 10048930

Crystal structure of the MAPK phosphatase Pyst1 catalytic domain and implications for regulated activation.

A.E.Stewart, S.Dowd, S.M.Keyse, N.Q.McDonald.

ABSTRACT

The crystal structure of the catalytic domain from the MAPK phosphatase Pyst1 (Pyst1-CD) has been determined at 2.35 A. The structure adopts a protein tyrosine phosphatase (PTPase) fold with a shallow active site that displays a distorted geometry in the absence of its substrate with some similarity to the dual-specificity phosphatase cdc25. Functional characterization of Pyst1-CD indicates it is sufficient to dephosphorylate activated ERK2 in vitro. Kinetic analysis of Pyst1 and Pyst1-CD using the substrate p-nitrophenyl phosphate (pNPP) reveals that both molecules undergo catalytic activation in the presence of recombinant inactive ERK2, switching from a low- to high-activity form. Mutation of Asp 262, located 5.5 A distal to the active site, demonstrates it is essential for catalysis in the high-activity ERK2-dependent conformation of Pyst1 but not for the low-activity ERK2-independent form, suggesting that ERK2 induces closure of the Asp 262 loop over the active site, thereby enhancing Pyst1 catalytic efficiency.

Selected figure(s)

Figure 3.
Figure 3. The chloride ion is shown as a cyan sphere, oxygen atoms of water molecules as red spheres and Trp 264 of a symmetry−related molecule is drawn in purple. b, Superposition of the PTP−loop, putative general acid loop and variable insert sequence of Pyst1−CD (standard element colors) with equivalent regions from VHR (green). Selected side chains for Pyst1−CD and VHR are shown and the Pyst1−CD side chains are labeled. Hydrogen bonds between the phosphate−binding Arg 130 of VHR and the carbonyl oxygen from residues 69 and 90 are shown. The chloride ion of Pyst1−CD is omitted for clarity. c, Superposition of the same regions and side chains of Pyst1−CD with PTP1B (purple). Arg 221 of PTP1B contacts Glu 115 and the carbonyl oxygen of residues 110 and 179. d, Superposition of equivalent regions of cdc25a with Pyst1−CD, highlighting Cys 430, Glu 431 and Arg 436 of cdc25a. Although the active sites of these phosphatases are similar, their topological folds are quite different^[297]5.The two structures have an r.m.s. difference of 1.89 Å for 55 C [298]alpha atoms This figure was prepared using SETOR^[299]32.

Figure 6.
Figure 6. A hypothetical model for the interaction of Pyst1 with ERK2. The structure of Pyst1−CD (green) was superposed onto the coordinates of PTP1B (PDB accession code 1PTV). Residue Tyr 185 of activated ERK2 was superposed onto a phospho−tyrosine substrate within the active site of PTP1B. This transformation was then applied to the entire coordinate set of activated ERK2 (PDB accession code 2ERK). Phosphorylated residues Thr 183 and Tyr 185 in addition to Asp 319 are highlighted on the ERK2 backbone (cyan). Mutation of Asp 319 to Asn in the Drosophila Sevenmaker MAPK leads to a MAPK that is resistant to and unable to interact with Pyst1 (10). We have made the assumption that Pyst1−ND makes contacts to Asp 319, and it is this interaction that is perturbed by the Sevenmaker mutant. A model for the Pyst1 amino−terminal domain (Pyst1−ND), based on cdc25 structure (PDB accession code 1CD25), is also shown in red, positioning the noncatalytic active site of Pyst1−ND to contact Asp 319. The connecting loop (residues 148−203) between the Pyst1−ND and Pyst1−CD domains is represented by white dots.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 174-181) copyright 1999.

Figures were selected by an automated process.