Three-dimensional structure of the diphtheria toxin repressor in complex with divalent cation co-repressors.
BACKGROUND
When Corynebacterium diphtheriae encounters an environment with a low concentration of iron ions, it initiates the synthesis of several virulence factors, including diphtheria toxin. The diphtheria toxin repressor (DtxR) plays a key role in this iron-dependent, global regulatory system and is the prototype for a new family of iron-dependent repressor proteins in Gram-positive bacteria. This study aimed to increase understanding of the general regulatory principles of cation binding to DtxR.


RESULTS
The crystal structure of dimeric DtxR holo-repressor in complex with different transition metals shows that each subunit comprises an amino-terminal DNA-binding domain, an interface domain (which contains two metal-binding sites) and a third, very flexible carboxy-terminal domain. Each DNA-binding domain contains a helix-turn-helix motif and has a topology which is very similar to catabolite gene activator protein (CAP). Molecular modeling suggests that bound DNA adopts a bent conformation with helices alpha 3 of DtxR interacting with the major grooves. The two metal-binding sites lie approximately 10 A apart. Binding site 2 is positioned at a potential hinge region between the DNA-binding and interface domains. Residues 98-108 appear to be crucial for the functioning of the repressor; these provide four of the ligands of the two metal-binding sites and three residues at the other side of the helix which are at the heart of the dimer interface.


CONCLUSIONS
The crystal structure of the DtxR holorepressor suggests that the divalent cation co-repressor controls motions of the DNA-binding domain. In this way the metal co-repressor governs the distance between operator recognition elements in the two subunits and, consequently, DNA recognition.
Qiu
X
X
Department of Biological Structure, School of Medicine, University of Washington, Seattle 98195, USA.
Verlinde
C L
CL
Zhang
S
S
Schmitt
M P
MP
Holmes
R K
RK
Hol
W G
WG
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D003198:Computer Simulation; D003353:Corynebacterium diphtheriae / Q000378:metabolism; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D018257:Helix-Loop-Helix Motifs; D046911:Macromolecular Substances; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012097:Repressor Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; C075586:DtxR protein, Corynebacterium diphtheriae; D046911:Macromolecular Substances; D012097:Repressor Proteins