Taxonomic distribution of proteins containing Trans_reg_C domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing Trans_reg_C domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

The DNA-binding domain of OmpR: crystal structures of a winged helixtranscription factor.

Martinez-Hackert E, Stock AM
Structure. 1997; 5: 109-24

BACKGROUND: The differential expression of the ompF and ompC genes isregulated by two proteins that belong to the two component family ofsignal transduction proteins: the histidine kinase, EnvZ, and the responseregulator, OmpR. OmpR belongs to a subfamily of at least 50 responseregulators with homologous C-terminal DNA-binding domains of approximately98 amino acids. Sequence homology with DNA-binding proteins of knownstructure cannot be detected, and the lack of structural information hasprevented understanding of many of this familys functional properties.RESULTS: We have determined the crystal structure of the Escherichia coliOmpR C-terminal domain at 1.95 A resolution. The structure consists ofthree alpha helices packed against two antiparallel beta sheets. Twohelices, alpha2 and alpha3, and the ten residue loop connecting themconstitute a variation of the helix-turn-helix (HTH) motif. Helix alpha3and the loop connecting the two C-terminal beta strands, beta6 and beta7,are probable DNA-recognition sites. Previous mutagenesis studies indicatethat the large loop connecting helices alpha2 and alpha3 is the site ofinteraction with the alpha subunit of RNA polymerase. CONCLUSIONS: OmpRcbelongs to the family of 'winged helix-turn-helix' DNA-binding proteins.This relationship, and the results from numerous published mutagenesisstudies, have helped us to interpret the functions of most of thestructural elements present in this protein domain. The structure of OmpRccould be useful in helping to define the positioning of the alpha subunitof RNA polymerase in relation to transcriptional activators that are boundto DNA.

A novel family of proteins that regulates antibiotic production instreptomycetes appears to contain an OmpR-like DNA-binding fold.

Wietzorrek A, Bibb M
Mol Microbiol. 1997; 25: 1181-4

Structure of the Escherichia coli response regulator NarL.

Baikalov I, Schroder I, Kaczor-Grzeskowiak M, Grzeskowiak K, Gunsalus RP, Dickerson RE
Biochemistry. 1996; 35: 11053-61

The crystal structure analysis of the NarL protein provides a first look at interactions between receiver and effector domains of a full-length bacterial response regulator. The N-terminal receiver domain, with 131 amino acids, is folded into a 5-strand beta sheet flanked by 5 alpha helices, as seen in CheY and in the N-terminal domain of NTRC. The C-terminal DNA-binding domain, with 62 amino acids, is a compact bundle of 4 alpha helices, of which the middle 2 form a helix-turn-helix motif closely related to that of Drosophila paired protein and other H-T-H DNA-binding proteins. The 2 domains are connected by an alpha helix of 10 amino acids and a 13-residue flexible tether that is not visible and presumably disordered in the X-ray structure. In this unphosphorylated form of NarL, the C-terminal domain is turned against the receiver domain in a manner that would preclude DNA binding. Activation of NarL via phosphorylation of Asp59 must involve transfer of information to the interdomain interface and either rotation or displacement of the DNA-binding C-terminal domain. Docking of a B-DNA duplex against the isolated C-terminal domain in the manner observed in paired protein and other H-T-H proteins suggests a stereochemical basis for DNA sequence preference: T-R-C-C-Y (high affinity) or T-R-C-T-N (low affinity), which is close to the experimentally observed consensus sequence: T-A-C-Y-N. The NarL structure is a model for other members of the FixJ or LuxR family of bacterial transcriptional activators, and possibly to the more distant OmpR and NtrC families as well.