PDBsum entry 3hyc

Hydrolase

PDB id: 3hyc

Contents

Protein chains

(+ 2 more) 181 a.a. *

Metals

_MG ×8

_CL ×5

* Residue conservation analysis

PDB id:

3hyc

Name:

Hydrolase

Title:

Crystal structure of e. Coli phosphatase yrbi, with mg, tetragonal form

Structure:

3-deoxy-d-manno-octulosonate 8-phosphate phosphatase. Chain: a, b, c, d, e, f, g, h. Synonym: kdo 8-p phosphatase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 37762. Strain: b. Gene: yrbi

Resolution:

3.06Å R-factor: 0.242 R-free: 0.257

Authors:

O.V.Tsodikov,T.Biswas

Key ref:

T.Biswas et al. (2009). The tail of KdsC: conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase. J Biol Chem, 284, 30594-30603. PubMed id: 19726684 DOI: 10.1074/jbc.M109.012278

Date:

22-Jun-09 Release date: 01-Sep-09

Protein chains

P67653  (KDSC_ECOL6) -  3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC from Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)

Seq: 188 a.a.

Struc: 181 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.3.45 - 3-deoxy-manno-octulosonate-8-phosphatase.
• Reaction: 3-deoxy-alpha-D-manno-2-octulosonate-8-phosphate + H2O = 3-deoxy-alpha-D- manno-oct-2-ulosonate + phosphate

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

Key reference

DOI no: 10.1074/jbc.M109.012278

J Biol Chem 284:30594-30603 (2009)

PubMed id: 19726684

The tail of KdsC: conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase.

T.Biswas, L.Yi, P.Aggarwal, J.Wu, J.R.Rubin, J.A.Stuckey, R.W.Woodard, O.V.Tsodikov.

ABSTRACT

The phosphatase KdsC cleaves 3-deoxy-D-manno-octulosonate 8-phosphate to generate a molecule of inorganic phosphate and Kdo. Kdo is an essential component of the lipopolysaccharide envelope in Gram-negative bacteria. Because lipopolysaccharide is an important determinant of bacterial resistance and toxicity, KdsC is a potential target for novel antibacterial agents. KdsC belongs to the broad haloacid dehalogenase superfamily. In haloacid dehalogenase superfamily enzymes, substrate specificity and catalytic efficiency are generally dictated by a fold feature called the cap domain. It is therefore not clear why KdsC, which lacks a cap domain, is catalytically efficient and highly specific to 3-deoxy-D-manno-octulosonate 8-phosphate. Here, we present a set of seven structures of tetrameric Escherichia coli KdsC (ranging from 1.4 to 3.06 A in resolution) that model different intermediate states in its catalytic mechanism. A crystal structure of product-bound E. coli KdsC shows how the interface between adjacent monomers defines the active site pocket. Kdo is engaged in a network of polar and nonpolar interactions with residues at this interface, which explains substrate specificity. Furthermore, this structural and kinetic analysis strongly suggests that the binding of the flexible C-terminal region (tail) to the active site makes KdsC catalytically efficient by facilitating product release.

Selected figure(s)

Figure 3.
A representative view of all seven tetrameric KdsC structures. The conformation of the active site (open or closed) for each monomer is specified. The positions of Mg^2+, Ca^2+, and Cl^− ions are shown as the red, purple, and orange spheres, respectively. Kdo8P (blue), Kdo (blue), and the phosphate (green) are shown as stick models. Captions designate the contents of each crystal forms, their space groups, and resolutions (for more details, see Tables 1 and 2). The compounds present in the crystallization mixture but not observed in the protein structure are written in parentheses.

Figure 4.
A, structure of the KdsC tetramer showing the relative disposition of the β-hairpins responsible for tetramerization. The Mg^2+ (red) and the Cl^− (orange) located in the catalytic cleft are shown as spheres. B, the side view of the tetramer with one monomer highlighted. C, the 1.4 Å |2F[o] − F[c]| electron density map of the active site contoured at 1σ. D, conformational differences between the open (magenta) and the closed (blue) conformations of the active site. The Kdo8P binding site is highlighted with a shadow. The tail of an adjacent monomer is colored black. res, residues.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 30594-30603) copyright 2009.

Figures were selected by an automated process.