PDBsum entry: 1utx

DNA-binding protein

PDB id: 1utx

Contents

Protein chains

66 a.a. *

Metals

IOD ×9

_NA

Waters ×193

* Residue conservation analysis

PDB id:

1utx

Name:

DNA-binding protein

Title:

Regulation of cytolysin expression by enterococcus faecalis: role of cylr2

Structure:

Cylr2. Chain: a, b. Engineered: yes

Source:

Enterococcus faecalis. Organism_taxid: 1351. Strain: fa2-2(pam714). Atcc: 19433. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: dsm 20478, ncdo 581, ncib 775, nctc 775

Biol. unit:

Dimer (from PDB file)

Resolution:

1.90Å R-factor: 0.155 R-free: 0.193

Authors:

A.Razeto,S.Rumpel,C.M.Pillar,M.S.Gilmore,S.Becker, M.Zweckstetter

Key ref:

S.Rumpel et al. (2004). Structure and DNA-binding properties of the cytolysin regulator CylR2 from Enterococcus faecalis. EMBO J, 23, 3632-3642. PubMed id: 15359276 DOI: 10.1038/sj.emboj.7600367

Date:

12-Dec-03 Release date: 16-Sep-04

Protein chains

Q8VL32  (Q8VL32_ENTFA) -  CylR2

Seq: 66 a.a.

Struc: 66 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: DNA binding (2 terms)

DOI no: 10.1038/sj.emboj.7600367

EMBO J 23:3632-3642 (2004)

PubMed id: 15359276

Structure and DNA-binding properties of the cytolysin regulator CylR2 from Enterococcus faecalis.

S.Rumpel, A.Razeto, C.M.Pillar, V.Vijayan, A.Taylor, K.Giller, M.S.Gilmore, S.Becker, M.Zweckstetter.

ABSTRACT

Enterococcus faecalis is one of the major causes for hospital-acquired antibiotic-resistant infections. It produces an exotoxin, called cytolysin, which is lethal for a wide range of Gram-positive bacteria and is toxic to higher organisms. Recently, the regulation of the cytolysin operon was connected to autoinduction by a quorum-sensing mechanism involving the CylR1/CylR2 two-component regulatory system. We report here the crystal structure of CylR2 and its properties in solution as determined by heteronuclear NMR spectroscopy. The structure reveals a rigid dimer containing a helix-turn-helix DNA-binding motif as part of a five-helix bundle that is extended by an antiparallel beta-sheet. We show that CylR2 is a DNA-binding protein that binds specifically to a 22 bp fragment of the cytolysin promoter region. NMR chemical shift perturbation experiments identify surfaces involved in DNA binding and are in agreement with a model for the CylR2/DNA complex that attributes binding specificity to a complex network of CylR2/DNA interactions. Our results propose a mechanism where repression is achieved by CylR2 obstruction of the promoter preventing biosynthesis of the cytolysin operon transcript.

Selected figure(s)

Figure 5.
Figure 5 Dimer interface of CylR2. (A) Residues 1 -5 and 40 -65 of subunits A and B are colored red and green. Side chains of the predominantly hydrophobic residues Ile2, Pro41, Leu43, Ala46, Leu47, Lys48, Tyr51, Leu57, Phe61, Trp63 and Pro65 are shown. The orientation corresponds to Figure 3A. (B) Residues 40 -60 of CylR2 (red/green) are superimposed on residues 55 -74 of GerE (blue). The orientation corresponds to Figure 3B.

Figure 10.
Figure 10 (A) Overall model of the CylR2/DNA complex structure. (B) Detailed stereo view indicating important protein -DNA interactions in the major groove. The DNA is shown with the sense strand in yellow and the antisense strand in cyan. Side chains of CylR2 and nucleobases interacting by van der Waals contacts and/or hydrogen bonds are indicated.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 3632-3642) copyright 2004.

Figures were selected by an automated process.