PDBsum entry 3da3

Antibiotic

PDB id: 3da3

Contents

Protein chains

270 a.a.

Metals

_MG ×2

Waters ×144

PDB id:

3da3

Name:

Antibiotic

Title:

Crystal structure of colicin m, a novel phosphatase specifically imported by escherichia coli

Structure:

Colicin-m. Chain: a, b. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.50Å R-factor: 0.238 R-free: 0.295

Authors:

K.Zeth,R.Albrecht,C.Romer,V.Braun

Key ref:

K.Zeth et al. (2008). Crystal structure of colicin M, a novel phosphatase specifically imported by Escherichia coli. J Biol Chem, 283, 25324-25331. PubMed id: 18640984 DOI: 10.1074/jbc.M802591200

Date:

28-May-08 Release date: 02-Sep-08

Protein chains

P05820  (CEAM_ECOLX) -  Colicin-M from Escherichia coli

Seq: 271 a.a.

Struc: 270 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1074/jbc.M802591200

J Biol Chem 283:25324-25331 (2008)

PubMed id: 18640984

Crystal structure of colicin M, a novel phosphatase specifically imported by Escherichia coli.

K.Zeth, C.Römer, S.I.Patzer, V.Braun.

ABSTRACT

Colicins are cytotoxic proteins secreted by certain strains of Escherichia coli. Colicin M is unique among these toxins in that it acts in the periplasm and specifically inhibits murein biosynthesis by hydrolyzing the pyrophosphate linkage between bactoprenol and the murein precursor. We crystallized colicin M and determined the structure at 1.7A resolution using x-ray crystallography. The protein has a novel structure composed of three domains with distinct functions. The N-domain is a short random coil and contains the exposed TonB box. The central domain includes a hydrophobic alpha-helix and binds presumably to the FhuA receptor. The C-domain is composed of a mixed alpha/beta-fold and forms the phosphatase. The architectures of the individual modules show no similarity to known structures. Amino acid replacements in previously isolated inactive colicin M mutants are located in the phosphatase domain, which contains a number of surface-exposed residues conserved in predicted bacteriocins of other bacteria. The novel phosphatase domain displays no sequence similarity to known phosphatases. The N-terminal and central domains are not conserved among bacteriocins, which likely reflect the distinct import proteins required for the uptake of the various bacteriocins. The homology pattern supports our previous proposal that colicins evolved by combination of distinct functional domains.

Selected figure(s)

Figure 3.
FIGURE 3. Similarities of colicin M to other protein structures. A, simulated annealed 2F[o] - F[c] map of the N-terminal TonB-box domain. B, superposition of the N termini of colicin M (white), FhuA (magenta; in complex with a TonB fragment; PDB entry 2GRX), and BtuB (cyan; in complex with a TonB fragment; PDB entry 2GSK). C, superposition of the C-terminal domain of colicin M (gray) with the membrane-spanning part of the outer membrane transporter Hia of H. influenzae (red, blue, and green) (39).

Figure 5.
FIGURE 5. Tentative model of colicin M uptake across the outer membrane (OM) of E. coli. I, colicin M (crystal structure) binds to the FhuA protein, whose crystal structure is shown. II, colicin M partially unfolds while bound to FhuA. III, N-terminal domain (red) with the TonB box (yellow) enters the pore in FhuA, which is formed by interaction of FhuA with energized TonB (green), leading to movement of the globular domain (cork) out of FhuA. IV, TonB box of colicin M interacts with TonB, and colicin M unfolds further and enters the periplasm through the FhuA pore. VI, in the periplasm, colicin M is refolded with the help of the FkpA chaperon and cleaves the pyrophosphate bond between C55 isoprenoid and the murein precursor. IM, inner membrane; , membrane potential. For the sake of clarity, the ExbB and ExbD proteins associated with TonB and required for TonB activity are not shown.

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 25324-25331) copyright 2008.

Figures were selected by an automated process.