DeoRC

DeoR C terminal sensor domain

• SMART accession number: SM01134
• Description: The sensor domains of the DeoR are catalytically inactive versions of the ISOCOT fold, but retain the substrate binding site ((PUBMED:16376935)). DeorC senses diverse sugar derivatives such as deoxyribose nucleoside (DeoR), tagatose phosphate (LacR), galactosamine (AgaR), myo-inositol (Bacillus IolR) and L-ascorbate (UlaR) ((PUBMED:16376935), 18844374, 15306018).

There are 40447 DeoRC domains in 40447 proteins in SMART's nrdb database.

Cellular role (predicted cellular role)

Cellular role: metabolism

Literature (relevant references for this domain)

Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

• Garces F et al.
• Quaternary structural transitions in the DeoR-type repressor UlaR controltranscriptional readout from the L-ascorbate utilization regulon in Escherichiacoli.
• Biochemistry. 2008; 47: 11424-33

UlaR is a DNA binding protein of the DeoR family of eubacterial transcriptionalrepressors which maintains the utilization of the L-ascorbate ula regulon in arepressed state. The availability of L-ascorbate in the growth medium releasesUlaR-mediated repression on the ula regulon, thereby activating transcription.The molecular details of this induction by L-ascorbate have remained elusive todate. Here we have identified L-ascorbate 6-phosphate as a direct effector ofUlaR; using a combination of site-directed mutagenesis, gel retardation,isothermal titration calorimetry, and analytical ultracentrifugation studies, we have identified the key amino acid residues that mediate L-ascorbate 6-phosphate binding and constructed the first model of regulation of a DeoR family member,establishing the basis of the ula regulon transcription control by UlaR. In this model, specific quaternary rearrangements of the DeoR-type repressor are themolecular underpinning of the activating and repressing forms. A DNA-bound UlaRtetramer establishes repression, whereas an L-ascorbate-6-phosphate-inducedbreakdown of the tetrameric configuration in favor of an UlaR dimeric stateresults in dissociation of UlaR from DNA and allows transcription of ulaG and ulaABCDEF structural genes. Despite the fact that similar changes have beendescribed for other unrelated repressor factors, this is the first report todemonstrate that specific oligomerization changes are responsible for theactivating and repressing forms of a DeoR-type eubacterial transcriptionalrepressor.

• Anantharaman V, Aravind L
• Diversification of catalytic activities and ligand interactions in the proteinfold shared by the sugar isomerases, eIF2B, DeoR transcription factors, acyl-CoA transferases and methenyltetrahydrofolate synthetase.
• J Mol Biol. 2006; 356: 823-42

Evolution of diverse catalytic and ligand-binding activities in a given proteinfold is a widely observed phenomenon in the protein-domain universe. However, thedetails of this evolutionary process, general principles, if any, andimplications for origins of particular catalytic mechanisms are poorly understoodin many common protein folds. Taking advantage of the wealth of currentlyavailable protein structure and sequence data, we explore these issues in thecontext of a large assemblage of biochemically diverse protein domains sharing a common origin, namely the sugar isomerases, translation factor eIF2B,ligand-binding domains of the DeoR-family transcription factors, acetyl-CoAtransferases and methenyltetrahydrofolate synthetase. We show that in at leastthree independent instances, including the sugar-binding domains of the DeoRfamily transcription factors, this domain has been used as small molecule sensor coupled to helix-turn-helix DNA-binding domains. In at least two of theseinstances the domain functions as a non-catalytic sensor of ligands. We provideevidence that the ancestral version of this fold was a distinct version of theRosmann-like folds, which probably possessed two distinct ligand-binding areasthat were differentially utilized in different descendents. Analyzing thesequences and structures of proteins in this fold we show that there are twoprincipal factors related to the origin of catalytic diversity in this fold.Firstly, specific inserts and extension added to the core domain on multipleoccasions in evolution have affected the access to the active site regions, andthereby allowed for different substrates and allosteric regulators. The secondmajor factor appears to be the emergence of considerable diversity offamily-specific residues with important biochemical roles. Interestingly,proteins of this fold, which catalyze similar reactions on similar substrates,might possess very distinctive sets of active residues required for substratebinding catalysis. In particular, different sugar isomerases or acyl transferasesin this fold might show distinct constellations of active site residues. Thesefindings suggest that whereas ligand-binding, and even generic catalytic ability emerged early in the evolution of the fold, the specific catalytic mechanismsappear to have independently emerged on multiple occasions in the genericprecursors of this fold.

• Muller FH, Bandeiras TM, Urich T, Teixeira M, Gomes CM, Kletzin A
• Coupling of the pathway of sulphur oxidation to dioxygen reduction:characterization of a novel membrane-bound thiosulphate:quinone oxidoreductase.
• Mol Microbiol. 2004; 53: 1147-60

Thiosulphate is one of the products of the initial step of the elemental sulphur oxidation pathway in the thermoacidophilic archaeon Acidianus ambivalens. A novelthiosulphate:quinone oxidoreductase (TQO) activity was found in the membraneextracts of aerobically grown cells of this organism. The enzyme was purified21-fold from the solubilized membrane fraction. The TQO oxidized thiosulphatewith tetrathionate as product and ferricyanide or decyl ubiquinone (DQ) aselectron acceptors. The maximum specific activity with ferricyanide was 73.4 U(mg protein)(-1) at 92 degrees C and pH 6, with DQ it was 397 mU (mg protein)(-1)at 80 degrees C. The Km values were 2.6 mM for thiosulphate (k(cat) = 167 s(-1)),3.4 mM for ferricyanide and 5.87 micro M for DQ. The enzymic activity wasinhibited by sulphite (Ki = 5 micro M), metabisulphite, dithionite andTritonX-100, but not by sulphate or tetrathionate. A mixture of caldariellaquinone, sulfolobus quinone and menaquinone was non-covalently bound to theprotein. No other cofactors were detected. Oxygen consumption was measured inmembrane fractions upon thiosulphate addition, thus linking thiosulphateoxidation to dioxygen reduction, in what constitutes a novel activity amongArchaea. The holoenzyme was composed of two subunits of apparent molecular massesof 28 and 16 kDa. The larger subunit appeared to be glycosylated and wasidentical to DoxA, and the smaller was identical to DoxD. Both subunits had been described previously as a part of the terminal quinol:oxygen oxidoreductasecomplex (cytochrome aa3).

Links (links to other resources describing this domain)

• PFAM: DeoRC