PDBsum entry 1rlo

Hydrolase

PDB id: 1rlo

Contents

Protein chains

268 a.a. *

Ligands

GOL ×2

Metals

_MG ×4

Waters ×455

* Residue conservation analysis

PDB id:

1rlo

Name:

Hydrolase

Title:

Phospho-aspartyl intermediate analogue of ybiv from e. Coli k12

Structure:

Phosphatase. Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: ybiv, b0822. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.219 R-free: 0.251

Authors:

A.Roberts,S.Y.Lee,E.Mccullagh,R.E.Silversmith,D.E.Wemmer

Key ref:

A.Roberts et al. (2005). Ybiv from Escherichia coli K12 is a HAD phosphatase. Proteins, 58, 790-801. PubMed id: 15657928 DOI: 10.1002/prot.20267

Date:

26-Nov-03 Release date: 07-Dec-04

Protein chains

P75792  (SUPH_ECOLI) -  Sugar phosphatase YbiV from Escherichia coli (strain K12)

Seq: 271 a.a.

Struc: 268 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.1.3.23 - sugar-phosphatase.
• Reaction: sugar phosphate + H2O = sugar + phosphate

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

Key reference

DOI no: 10.1002/prot.20267

Proteins 58:790-801 (2005)

PubMed id: 15657928

Ybiv from Escherichia coli K12 is a HAD phosphatase.

A.Roberts, S.Y.Lee, E.McCullagh, R.E.Silversmith, D.E.Wemmer.

ABSTRACT

The protein YbiV from Escherichia coli K12 MG1655 is a hypothetical protein with sequence homology to the haloacid dehalogenase (HAD) superfamily of proteins. Although numerous members of this family have been identified, the functions of few are known. Using the crystal structure, sequence analysis, and biochemical assays, we have characterized YbiV as a HAD phosphatase. The crystal structure of YbiV reveals a two-domain protein, one with the characteristic HAD hydrolase fold, the other an inserted alpha/beta fold. In an effort to understand the mechanism, we also solved and report the structures of YbiV in complex with beryllofluoride (BeF3-) and aluminum trifluoride (AlF3), which have been shown to mimic the phosphorylated intermediate and transition state for hydrolysis, respectively, in analogy to other HAD phosphatases. Analysis of the structures reveals the substrate-binding cavity, which is hydrophilic in nature. Both structure and sequence homology indicate YbiV may be a sugar phosphatase, which is supported by biochemical assays that measured the release of free phosphate on a number of sugar-like substrates. We also investigated available genomic and functional data in an effort to determine the physiological substrate.

Selected figure(s)

Figure 1.
Figure 1. A: Ribbon diagram of the structure of YbiV. The hydrolase domain is colored in medium grey, the inserted domain in light grey. The nucleophilic aspartate and the magnesium ion are dark grey. B: Secondary structure topology of YbiV shaded similarly to A. C: Overlay of the hydrolase domains of PSP (pink) and YrbI (blue) onto the full structure of YbiV (grey), all as alpha carbon backbones. The full structures of the PSP and YrbI monomers (top and bottom, respectively) are shown to the right as ribbons. D: Surface potential plot of YbiV. Acidic regions are shown in red, basic regions in blue. (Fig.

Figure 3.
Figure 3. A: Stereoview of the native active-site of YbiV. The magnesium ion is represented by a magenta sphere, water molecules as blue spheres. Hydrogen bonds are represented as dashed lines and numbers indicate distances in Angstroms. The active-site motifs are labeled. B: Overlay of the active-sites of YrbI from H. influenzae (green) and YbiV (blue.) The blue sphere represents magnesium, the green sphere, cobalt. The residue numbers are labeled, YbiV on the left, YrbI on the right.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 58, 790-801) copyright 2005.

Figures were selected by an automated process.