PDBsum entry 4da1

Hydrolase

PDB id: 4da1

Contents

Protein chain

257 a.a.

Ligands

BME ×3

Metals

_MG ×3

Waters ×64

PDB id:

4da1

Name:

Hydrolase

Title:

Crystal structure of branched-chain alpha-ketoacid dehydrogenase phosphatase with mg (ii) ions at the active site

Structure:

Protein phosphatase 1k, mitochondrial. Chain: a. Fragment: truncated phosphatase protein (unp residues 84-360). Synonym: pp2c domain-containing protein phosphatase 1k, pp2c-like mitochondrial protein, pp2c-type mitochondrial phosphoprotein phosphatase, ptmp, protein phosphatase 2c isoform kappa, pp2c-kappa. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ppm1k, pp2cm. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.38Å R-factor: 0.178 R-free: 0.205

Authors:

C.A.Brautigam,J.L.Chuang,D.T.Chuang

Key ref:

R.M.Wynn et al. (2012). Structural and biochemical characterization of human mitochondrial branched-chain α-ketoacid dehydrogenase phosphatase. J Biol Chem, 287, 9178-9192. PubMed id: 22291014

Date:

12-Jan-12 Release date: 08-Feb-12

Protein chain

Q8N3J5  (PPM1K_HUMAN) -  Protein phosphatase Mn(2+)-dependent 1K from Homo sapiens

Seq: 372 a.a.

Struc: 257 a.a.

Enzyme reactions

• Enzyme class 1: E.C.3.1.3.16 - protein-serine/threonine phosphatase.
• Reaction:
  1. O-phospho-L-seryl-[protein] + H2O = L-seryl-[protein] + phosphate
  2. O-phospho-L-threonyl-[protein] + H2O = L-threonyl-[protein] + phosphate
• Enzyme class 2: E.C.3.1.3.52 - [3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)]-
• Reaction: O-phospho-L-seryl-[3-methyl-2-oxobutanoate dehydrogenase] + H2O = L-seryl-[3-methyl-2-oxobutanoate dehydrogenase] + 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

reference

J Biol Chem 287:9178-9192 (2012)

PubMed id: 22291014

Structural and biochemical characterization of human mitochondrial branched-chain α-ketoacid dehydrogenase phosphatase.

R.M.Wynn, J.Li, C.A.Brautigam, J.L.Chuang, D.T.Chuang.

ABSTRACT

The branched-chain α-ketoacid dehydrogenase phosphatase (BDP) component of the human branched-chain α-ketoacid dehydrogenase complex (BCKDC) has been expressed in Escherichia coli and purified in the soluble form. The monomeric BDP shows a strict dependence on Mn(2+) ions for phosphatase activity, whereas Mg(2+) and Ca(2+) ions do not support catalysis. Metal binding constants for BDP, determined by competition isothermal titration calorimetry, are 2.4 nm and 10 μm for Mn(2+) and Mg(2+) ions, respectively. Using the phosphorylated decarboxylase component (p-E1b) of BCKDC as a substrate, BDP shows a specific activity of 68 nmol/min/mg. The Ca(2+)-independent binding of BDP to the 24-meric transacylase (dihydrolipoyl transacylase; E2b) core of BCKDC results in a 3-fold increase in the dephosphorylation rate of p-E1b. However, the lipoyl prosthetic group on E2b is not essential for BDP binding or E2b-stimulated phosphatase activity. Acidic residues in the C-terminal linker of the E2b lipoyl domain are essential for the interaction between BDP and E2b. The BDP structure was determined by x-ray crystallography to 2.4 Å resolution. The BDP structure is dominated by a central β-sandwich. There are two protrusions forming a narrow cleft ∼10 Å wide, which constitutes the active site. The carboxylate moieties of acidic residues Asp-109, Asp-207, Asp-298, and Asp-337 in the active-site cleft participate in binding two metal ions. Substitutions of these residues with alanine nullify BDP phosphatase activity. Alteration of the nearby Arg-104 increases the K(m) for p-E1b peptide by 60-fold, suggesting that this residue is critical for the recognition of the native p-E1b protein.