These include Protein Data Bank (PDB) entry 3O0F (locus tag Bad1165 from Bifidobacterium adolescentis), PDB entry 2ANU (locus tag Tm0559 from Thermotoga maritima), and PDB entry 3E38 (locus tag Bvu3505 from Bacteroides vulgatus).
The genes encoding A9CG74 orthologs UniProt entry B3Q5L5 (locus tag RHECIAT_PC0000418 from Rhizobium etli strain CIAT 652) and UniProt entry B9JNP7 (locus tag Arad_7740 from Agrobacterium radiobacter strain K84) were cloned using ligation-independent cloning into a pAVITAG tagless vector.
Using a library of 77 acid sugars for high-throughput screening, one protein (UniProt entry A9CG74; locus tag Atu4196) showed activity with both m-galactarate and d-galacturonate.
This pathway is initiated by a uronate dehydrogenase that oxidizes d-galacturonate to d-galactaro-1,5-lactone (δ-galactarolactone); a lactone isomerase (GLI; UniProt entry A9CEQ7; locus tag Atu3138) then converts δ-galactarolactone to γ-galactarolactone, the substrate for Gci.
In this work, we describe the assignment of the in vitro enzymatic activity to UniProt entry A9CG74 (locus tag Atu4196), a functionally uncharacterized member of the MR subgroup, which is encoded by the A. tumefaciens C58 genome.
For example, Gci (UniProt entry A9CEQ8; locus tag Atu3139), a member of the MR subgroup of the ENS, recently was shown to catalyze the novel cycloisomerization of d-galactaro-1,4-lactone (γ-galactarolactone) to 5-keto-4-deoxy d-galactarate in a pathway for degradation of d-galacturonate, the major component of pectin found in plant cell walls.
Three methods have shown some potential in this direction, the so-called spoligotyping assay (Mycobacterium tuberculosis, 40,000 entries database), Multiple Loci Sequence Typing (MLST; up to a few thousands entries for the more than 20 bacterial species), and more recently Multiple Loci VNTR Analysis (MLVA; up to a few hundred entries, assays available for more than 20 pathogens).
The primary transcripts are positioned at the top of each locus entry.
Once matched, all PubMed entries associated with the gi number were automatically transferred to the locus entry.
The RefSeq table includes calculations aimed at extracting several key features of the GenBank RefSeq entry: in particular, LOCUS and 5' UTR length.
