The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649  92 GVVSVSLPPATAAHLVMPHLGKFYRQYPELQLRILGDVHYASLQHREADIAVRFGRPKDDYLIARKAGEVPFGIYAAQEY 171
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649 172 LDA-------------------IQEENYEWISVEVGGVQGQKQqklkqrlnykEPVMVTNHPELQWRATCGAVGLAVLPD 232
Cdd:cd08422   81 LARhgtpqtpedlarhrclgyrLPGRPLRWRFRRGGGEVEVRV----------RGRLVVNDGEALRAAALAGLGIALLPD 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 598589649 233 FLG----QQGHLVK-LPDDDPMSAEIWLVIHEDLRSSPAVRVVMDFL 274
Cdd:cd08422  151 FLVaedlASGRLVRvLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649   91 SGVVSVSLPPATAAHLVMPHLGKFYRQYPELQLRIL---GDVHYASLQHREADIAVRFGRPKDDYLIARKAGEVPFGIYA 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTegnSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649  168 AQEY-------LDAIQEENYEWISVEVGGVQGQKQQKLKQRLNYK-EPVMVTNHPELQWRATCGAVGLAVLPDFLGQ--- 236
Cdd:pfam03466  81 PPDHplargepVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRpRVVLEVNSLEALLQLVAAGLGIALLPRSAVArel 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 598589649  237 -QGHLVKLP-DDDPMSAEIWLVIHEDLRSSPAVRVVMDFLLD 276
Cdd:pfam03466 161 aDGRLVALPlPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649  92 GVVSVSLPPATAAHLVMPHLGKFYRQYPELQLRILGDVHYASLQHREADIAVRFGRPKDDYLIARKAGEVPFGIYAAQEY 171
Cdd:cd08422    1 GRLRISAPVSFGRLHLAPLLAEFLARYPDVRLELVLSDRLVDLVEEGFDLAIRIGELPDSSLVARRLGPVRRVLVASPAY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649 172 LDA-------------------IQEENYEWISVEVGGVQGQKQqklkqrlnykEPVMVTNHPELQWRATCGAVGLAVLPD 232
Cdd:cd08422   81 LARhgtpqtpedlarhrclgyrLPGRPLRWRFRRGGGEVEVRV----------RGRLVVNDGEALRAAALAGLGIALLPD 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 598589649 233 FLG----QQGHLVK-LPDDDPMSAEIWLVIHEDLRSSPAVRVVMDFL 274
Cdd:cd08422  151 FLVaedlASGRLVRvLPDWRPPPLPIYAVYPSRRHLPAKVRAFIDFL 197

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649   91 SGVVSVSLPPATAAHLVMPHLGKFYRQYPELQLRIL---GDVHYASLQHREADIAVRFGRPKDDYLIARKAGEVPFGIYA 167
Cdd:pfam03466   1 SGRLRIGAPPTLASYLLPPLLARFRERYPDVELELTegnSEELLDLLLEGELDLAIRRGPPDDPGLEARPLGEEPLVLVA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649  168 AQEY-------LDAIQEENYEWISVEVGGVQGQKQQKLKQRLNYK-EPVMVTNHPELQWRATCGAVGLAVLPDFLGQ--- 236
Cdd:pfam03466  81 PPDHplargepVSLEDLADEPLILLPPGSGLRDLLDRALRAAGLRpRVVLEVNSLEALLQLVAAGLGIALLPRSAVArel 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 598589649  237 -QGHLVKLP-DDDPMSAEIWLVIHEDLRSSPAVRVVMDFLLD 276
Cdd:pfam03466 161 aDGRLVALPlPEPPLPRELYLVWRKGRPLSPAVRAFIEFLRE 202

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649  92 GVVSVSLPPATAAHLVMPHLGKFYRQYPELQLRI-LGDvHYASLQHREADIAVRFGRPKDDYLIARKAGEVPFGIYAAQE 170
Cdd:cd08472    1 GRLRVDVPGSLARLLLIPALPDFLARYPDIELDLgVSD-RPVDLIREGVDCVIRVGELADSSLVARRLGELRMVTCASPA 79

                 ....
gi 598589649 171 YLDA 174
Cdd:cd08472   80 YLAR 83

The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of 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. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649  94 VSVSLPPATAAHLVMPHLGKFYRQYPELQLRIL---GDVHYASLQHREADIAVRFGRPKDDYLIARKAGEVPFGIYAAQE 170
Cdd:cd05466    2 LRIGASPSIAAYLLPPLLAAFRQRYPGVELSLVeggSSELLEALLEGELDLAIVALPVDDPGLESEPLFEEPLVLVVPPD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649 171 YLDAIQEE-------NYEWISVEVGGVQGQKQQKLKQRLNYK-EPVMVTNHPELQWRATCGAVGLAVLPDF---LGQQGH 239
Cdd:cd05466   82 HPLAKRKSvtladlaDEPLILFERGSGLRRLLDRAFAEAGFTpNIALEVDSLEAIKALVAAGLGIALLPESaveELADGG 161

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 598589649 240 LVKLP-DDDPMSAEIWLVIHEDLRSSPAVRVVMDFL 274
Cdd:cd05466  162 LVVLPlEDPPLSRTIGLVWRKGRYLSPAARAFLELL 197

HTH-type transcriptional activator AaeR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649   5 ENLHYFSVFS---EEKTLSAAARKLGVDHATVARRIAQLEDNLKLKLVDRRPRTYILTSEGERLAKIVTRMMEETFSIER 81
Cdd:PRK10632   2 ERLKRMSVFAkvvEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649  82 LAQAGQQEISGVVSVSLPPATAAHLVMPHLGKFYRQYPELQLRILGDVHYASLQHREADIAVRFGRPKDDYLIARKAGEV 161
Cdd:PRK10632  82 QLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGALQDSSLFSRRLGAM 161

                        170
                 ....*....|.
gi 598589649 162 PFGIYAAQEYL 172
Cdd:PRK10632 162 PMVVCAAKSYL 172

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649  92 GVVSVSLPPATAAHLVMPHLGKFYRQYPELQLRI-LGDvHYASLQHREADIAVRFGRPKD-DYLIARKAGEVPFGIYAAQ 169
Cdd:cd08475    1 GRLRIDLPVAFGRLCVAPLLLELARRHPELELELsFSD-RFVDLIEEGIDLAVRIGELADsTGLVARRLGTQRMVLCASP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649 170 EYL---------------DAI----QEENYEWISVEVGGVQGQKQQklkqrlnykEPVMVTNHPELQWRATCGAVGLAVL 230
Cdd:cd08475   80 AYLarhgtprtledlaehQCIaygrGGQPLPWRLADEQGRLVRFRP---------APRLQFDDGEAIADAALAGLGIAQL 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 598589649 231 PDFLG----QQGHLVK-LPDDDPMSAEIWLVIHEDLRSSPAVRVVMDFL 274
Cdd:cd08475  151 PTWLVadhlQRGELVEvLPELAPEGLPIHAVWPRTRHLPPKVRAAVDAL 199

The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649  93 VVSVSLPPATAAHLVMPHLGKFYRQYPELQLRILGDVHYASLQHREADIAVRFGRPKDDYLIARKAGEVPFGIYAAQEYL 172
Cdd:cd08432    1 VLTVSVTPSFAARWLIPRLARFQARHPDIDLRLSTSDRLVDFAREGIDLAIRYGDGDWPGLEAERLMDEELVPVCSPALL 80

                 ..
gi 598589649 173 DA 174
Cdd:cd08432   81 AG 82

The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold; The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649  96 VSLPPATAAHLVMPHLGKFYRQYPELQLRILGDVHYASLQHREADIAVRFGRPKDDYLIARKAGEVPFGIYAAQEYLDA- 174
Cdd:cd08483    4 VTLTPSFASNWLMPRLGSFWAKHPEIELSLLPSADLVDLRPDGIDVAIRYGNGDWPGLESEPLTAAPFVVVAAPGLLGDr 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649 175 -------------IQE--ENYEWISVEVGGVQGQkqqklkqrlnyKEPVMVTNHPELQWRATCGAVGLAVLPDFLGQQ-- 237
Cdd:cd08483   84 kvdsladlaglpwLQErgTNEQRVWLASMGVVPD-----------LERGVTFLPGQLVLEAARAGLGLSIQARALVEPdi 152

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 598589649 238 --GHLVKLPDDDPMSAEIWLViHEDLRSSPAVRVVMDFL 274
Cdd:cd08483  153 aaGRLTVLFEEEEEGLGYHIV-TRPGVLRPAAKAFVRWL 190

CysB family HTH-type transcriptional regulator;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649  19 LSAAARKLGVDHATVARRIAQLEDNLKLKLVDRR-PRTYILTSEGERLAKIVTRMMEETFSIERLAQAGQQEISGVVSV- 96
Cdd:PRK12684  19 LTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHgKRLRGLTEPGRIILASVERILQEVENLKRVGKEFAAQDQGNLTIa 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 598589649  97 --------SLPPATAAhlvmphlgkFYRQYPELQLRIL-GDVHYAS--LQHREADIAV 143
Cdd:PRK12684  99 tthtqaryALPAAIKE---------FKKRYPKVRLSILqGSPTQIAemVLHGQADLAI 147

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649 107 VMPHLGKFYRQYPELQLRILGDVHYASLQHREADIAVRFGRPKDDYLIARKAGEVPFGIYAAQEYLDA------------ 174
Cdd:cd08479   16 IAPALSDFAKRYPELEVQLELTDRPVDLVEEGFDLDIRVGDLPDSSLIARKLAPNRRILCASPAYLERhgapaspedlar 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649 175 -----IQEENYE---WISVEVGGvqgqkqqKLKQRLNykePVMVTNHPE--LQWrATCGAvGLA------VLPDFlgQQG 238
Cdd:cd08479   96 hdclvIRENDEDfglWRLRNGDG-------EATVRVR---GALSSNDGEvvLQW-ALDGH-GIIlrsewdVAPYL--RSG 161

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 598589649 239 HLVK-LPDDDPMSAEIWLVIHEDLRSSPAVRVVMDFL 274
Cdd:cd08479  162 RLVRvLPDWQLPDADIWAVYPSRLSRSARVRVFVDFL 198

HTH-type transcriptional regulator ArgP;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649   1 MIDWENLHYFSVFSEEKTLSAAARKLGVDHATVARRIAQLEDNLKLKLVdRRPRTYILTSEGERLAKIVT--RMME-ETF 77
Cdd:PRK13348   1 MLDYKQLEALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLL-VRGRPCRPTPAGQRLLRHLRqvALLEaDLL 79

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 598589649  78 SIERLAQAGQQEIS-GVVSVSL----PPATAAHLVMPHL 111
Cdd:PRK13348  80 STLPAERGSPPTLAiAVNADSLatwfLPALAAVLAGERI 118

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649  92 GVVSVSLPPATAAHLVMPHLGKFYRQYPELQLRILGDVHYASLQHREADIAVRFGRPKDDYLIARKAGEVPFGIYAAQEY 171
Cdd:cd08477    1 GKLRISAPVTFGSHVLTPALAEYLARYPDVRVDLVLSDRLVDLVEEGFDAAFRIGELADSSLVARPLAPYRMVLCASPDY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649 172 L----------DAIQEE---------NYEWISVEVGGVQGQKQqklkqrlnykEPVMVTNHPELQWRATCGAVGLAVLPD 232
Cdd:cd08477   81 LarhgtpttpeDLARHEclgfsywraRNRWRLEGPGGEVKVPV----------SGRLTVNSGQALRVAALAGLGIVLQPE 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 598589649 233 FLG----QQGHLVK-LPDDDPMSAEIWLVIHEDLRSSPAVRVVMDFL 274
Cdd:cd08477  151 ALLaedlASGRLVElLPDYLPPPRPMHLLYPPDRRPTPKLRSFIDFL 197

HTH-type transcriptional activator IlvY;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649  32 TVARRIAQLEDNLKLKLVDRRPRTYILTSEGERLAKIVTRMMEETFSIERLAQAGQQEISGVVSV--SLppaTAA--HLv 107
Cdd:PRK11716   7 TLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLRHTLDQQGPSLSGELSLfcSV---TAAysHL- 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 598589649 108 mPH-LGKFYRQYPELQLRIL-GDVHYA--SLQHREADIAV 143
Cdd:PRK11716  83 -PPiLDRFRAEHPLVEIKLTtGDAADAveKVQSGEADLAI 121

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 10. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649  92 GVVSVSLPPATAAHLVMPHLGKFYRQYPELQLRILGDVHYASLQHREADIAVRFGRPKDDYLIARKAGEVPFGIYAAQEY 171
Cdd:cd08480    1 GRLRVNASVPFGTHFLLPLLPAFLARYPEILVDLSLTDEVVDLLAERTDVAIRVGPLPDSSLVARKLGESRRVIVASPSY 80

                 .
gi 598589649 172 L 172
Cdd:cd08480   81 L 81

transcriptional regulator CysB-like protein; Reviewed

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649  19 LSAAARKLGVDHATVARRIAQLEDNLKLKLVDRR-PRTYILTSEGERLAKIVTRMMEETFSIERLAQ--AGQQEISGVVS 95
Cdd:PRK12683  19 LTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRgKRLTGLTEPGKELLQIVERMLLDAENLRRLAEqfADRDSGHLTVA 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 598589649  96 VSlppATAAHLVMPHLGK-FYRQYPELQLRIlgdvHYAS-------LQHREADIAV 143
Cdd:PRK12683  99 TT---HTQARYALPKVVRqFKEVFPKVHLAL----RQGSpqeiaemLLNGEADIGI 147

transcriptional regulator CysB-like protein; Reviewed

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649  19 LSAAARKLGVDHATVARRIAQLEDNLKLKLVDRR-PRTYILTSEGERLAKIVTRMMEETFSIERLAQAGQQEISGVVSVS 97
Cdd:PRK12682  19 LTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHgKRLKGLTEPGKAVLDVIERILREVGNIKRIGDDFSNQDSGTLTIA 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 598589649  98 LPPATAAHLVMPHLGKFYRQYPELQLRIlgdvHYAS-------LQHREADIAV 143
Cdd:PRK12682  99 TTHTQARYVLPRVVAAFRKRYPKVNLSL----HQGSpdeiarmVISGEADIGI 147

nitrogen assimilation transcriptional regulator; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 598589649   7 LHYFSVFSEEKTLSAAARKLGVDHATVARRIAQLEDNLKLKLVDRRPRTYILTSEGERL---AKIVTRMMEEtfsierlA 83
Cdd:PRK11233   6 LKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILythARAILRQCEQ-------A 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 598589649  84 Q-----AGQqEISGVVSVSLPPATAAH-LVMPHLGKFYRQYPELQL 123
Cdd:PRK11233  79 QlavhnVGQ-ALSGQVSIGLAPGTAASsLTMPLLQAVRAEFPGIVL 123