>gnl|CDD|176107 cd08415, PBP2_LysR_opines_like, The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 196

 Score = 37.9 bits (89), Expect = 0.003
 Identities = 31/168 (18%), Positives = 53/168 (31%), Gaps = 38/168 (22%)

Query: 95  LRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDIS---MDY-----ADCAIRL 146
           LRIA    L  +LL   +  F   +PD++I L         S   ++      AD  +  
Sbjct: 2   LRIAALPALALSLLPRAIARFRARHPDVRISL-----HTLSSSTVVEAVLSGQADLGL-A 55

Query: 147 RKPIQSSSLIQRKLVTIHM-------HAYAAPHYLKNCREPLSIQELDKHNLITFGDLIP 199
             P+    L    L +          H  A        ++ ++  +L    LI+ G   P
Sbjct: 56  SLPLDHPGLESEPLASGRAVCVLPPGHPLAR-------KDVVTPADLAGEPLISLGRGDP 108

Query: 200 KCMEDFNWLATVD---RPIGEPRISCLQVNSYLSIMQYCVLGSGIALL 244
                      VD      G      ++     +       G G+A++
Sbjct: 109 LRQR-------VDAAFERAGVEPRIVIETQLSHTACALVAAGLGVAIV 149