PDBsum entry 2a4x

Antimicrobial protein

PDB id: 2a4x

Contents

Protein chains

131 a.a. *

Ligands

BLM

Waters ×293

* Residue conservation analysis

PDB id:

2a4x

Name:

Antimicrobial protein

Title:

Crystal structure of mitomycin c-binding protein complexed with metal- free bleomycin a2

Structure:

Mitomycin-binding protein. Chain: a, b. Engineered: yes

Source:

Streptomyces caespitosus. Organism_taxid: 53502. Gene: mrd. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.40Å R-factor: 0.222 R-free: 0.264

Authors:

N.Danshiitsoodol,C.A.De Pinho,Y.Matoba,T.Kumagai,M.Sugiyama

Key ref:

N.Danshiitsoodol et al. (2006). The mitomycin C (MMC)-binding protein from MMC-producing microorganisms protects from the lethal effect of bleomycin: crystallographic analysis to elucidate the binding mode of the antibiotic to the protein. J Mol Biol, 360, 398-408. PubMed id: 16756991 DOI: 10.1016/j.jmb.2006.05.017

Date:

30-Jun-05 Release date: 18-Jul-06

Protein chains

O05205  (O05205_STRLA) -  Mitomycin-binding protein from Streptomyces lavendulae

Seq: 130 a.a.

Struc: 131 a.a.

DOI no: 10.1016/j.jmb.2006.05.017

J Mol Biol 360:398-408 (2006)

PubMed id: 16756991

The mitomycin C (MMC)-binding protein from MMC-producing microorganisms protects from the lethal effect of bleomycin: crystallographic analysis to elucidate the binding mode of the antibiotic to the protein.

N.Danshiitsoodol, C.A.de Pinho, Y.Matoba, T.Kumagai, M.Sugiyama.

ABSTRACT

Antibiotic-producing microorganisms must be protected from the lethal effect of their own antibiotic. We have previously determined the X-ray crystal structure of the bleomycin (Bm)-binding protein, designated BLMA, as a self-resistance determinant from Bm-producing Streptomyces verticillus, which suggests that the binding of the first Bm to one of two pockets formed in the BLMA homodimer induces the cooperative binding of the second Bm to the other pocket. In the present study, we noticed that the X-ray crystallographic structure of a self-resistance determinant from a mitomycin C-producing microorganism, designated MRDP, reveals similarity to the folding pattern on the BLMA, although no sequence homology exists. To clarify the hypothesis that MRDP may function as a resistance determinant to Bm, we characterized and determined the crystal structure of MRDP complexed with the Cu(II)-bound form of BmA(2) grouped into the Bm family of antibiotics. The biochemical and structural studies for Bm binding provide evidence that the first Bm binds anti-cooperatively to a pocket of MRDP with binding affinity of the nanomolar order, whereas the second Bm binds to the other pocket, which has binding affinity of the micromolar order. The invisibility of the second Bm in the structure agrees with the observation that Escherichia coli-expressing MRDP displays lower resistance to Bm than that expressing BLMA. The structure of MRDP, which is complexed with the Cu(II)-bound BmA(2), revealed that the gamma-aminopropyldimethylsulphonium moiety of the antibiotic is sandwiched between the peripheral residues of the binding pocket and that its positively charged sulphonium head is accommodated completely in the negatively charged region of the MRDP pocket. Furthermore, the Cu(II)-bound BmA(2) has a very compact structure, in which the bithiazole ring of BmA(2) is folded back to the metal-binding domain.

Selected figure(s)

Figure 1.
Figure 1. Chemical structure of (a) BmA[2] and (b) MMC.

Figure 6.
Figure 6. A close-up view of Cu(II)-bound BmA[2] interaction at the binding pocket. Water molecules and Cu(II) ion are depicted as red spheres and a cyan ball, respectively. The side-chain of some important residues is drawn. Intermolecular and intramolecular hydrogen bonds <3.1 Å are shown as broken yellow lines, while penta-coordinated bonds of Cu(II) ion are represented by black dotted lines.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 360, 398-408) copyright 2006.

Figures were selected by an automated process.