The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 110 LLPKVVAEIRKQAPNMVVDIDSIPKRH-FEPLLSGDAHFVLSTHEPLSSEqnLYRMFVISRDYRLLMSKDHPLADKEITV 188
Cdd:cd08417   14 LLPPLLARLRQEAPGVRLRFVPLDRDDlEEALESGEIDLAIGVFPELPPG--LRSQPLFEDRFVCVARKDHPLAGGPLTL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 189 DDLLNSQLGQISLQGDKKLSIESRFKDLGLidkQRQlsIPIQLSNFNVAPDMAEATDIIFHLPTPFAQQAAKQRDLVCKR 268
Cdd:cd08417   92 EDYLAAPHVLVSPRGRGHGLVDDALAELGL---SRR--VALTVPHFLAAPALVAGTDLIATVPRRLAEALAERLGLRVLP 166

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 880813463 269 VPKALrhPSEDVYLYWHKRFHNDPMCRWVRNIFKEL 304
Cdd:cd08417  167 LPFEL--PPFTVSLYWHPRRDRDPAHRWLRELIAEL 200

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 110 LLPKVVAEIRKQAPNMVVDIDSIPKRH-FEPLLSGDAHFVLSTHEPLSSEqnLYRMFVISRDYRLLMSKDHPLADKEITV 188
Cdd:cd08417   14 LLPPLLARLRQEAPGVRLRFVPLDRDDlEEALESGEIDLAIGVFPELPPG--LRSQPLFEDRFVCVARKDHPLAGGPLTL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 189 DDLLNSQLGQISLQGDKKLSIESRFKDLGLidkQRQlsIPIQLSNFNVAPDMAEATDIIFHLPTPFAQQAAKQRDLVCKR 268
Cdd:cd08417   92 EDYLAAPHVLVSPRGRGHGLVDDALAELGL---SRR--VALTVPHFLAAPALVAGTDLIATVPRRLAEALAERLGLRVLP 166

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 880813463 269 VPKALrhPSEDVYLYWHKRFHNDPMCRWVRNIFKEL 304
Cdd:cd08417  167 LPFEL--PPFTVSLYWHPRRDRDPAHRWLRELIAEL 200

leucine transcriptional activator; Reviewed

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463   1 MNLAQVDLNLLVILKHLLEEKHVSNTALALDMSQPTVSRSLQKLRTVFNDDLLVRaaYGYELTPKAEAiKQDLNSVLTRL 80
Cdd:PRK09508  17 PQLRMVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVR--YGRGIQPTARA-RQLFGPVRQAL 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463  81 EkLVH----GDVFEPQTSDstvRFFGLV---PQVSHLLPKVVAEIRKQAPNMVVDIDSIPKRHFEPLLS-GDAHFVLSTH 152
Cdd:PRK09508  94 Q-LVQnelpGSGFEPESSE---RVFNLCicsPLDIRLTSQIYNRIEQIAPNIHVVFKSSLNQNIEHQLRyQETEFVISYE 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 153 EPLSSEQNLYRMFviSRDYRLLMSKDHPLADKEITVDDLLNSQLGQISLqgDKKLSiesrFKDLGLIDKQRQLSIPIQLS 232
Cdd:PRK09508 170 EFDRPEFTSVPLF--KDELVLVASKNHPRIKGPITEEQLYNEQHAVVSL--DRFAS----FSQPWYDTVDKQASIAYQGT 241

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 880813463 233 NFNVAPDMAEATDIIFHLPTPFAQQAAKQRDLvcKRVPKALRHPSEDVYLYWHKRFHNDPMCRWVRNIFKEL 304
Cdd:PRK09508 242 ALSSVLNVVSQTHLVAIAPRWLAEEFAESLEL--QILPLPLKNNSRTCYLSWHESAGRDKGHQWMEELLVSI 311

Bacterial regulatory helix-turn-helix protein, lysR family;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463    8 LNLLVILKHLLEEKHVSNTALALDMSQPTVSRSLQKLRTVFNDDLLVRAAYGYELTPKAE 67
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463   7 DLNLLVILKHLLEEKHVSNTALALDMSQPTVSRSLQKLRTVFNDDLLVRAAYGYELTPKAEAI----------KQDLNSV 76
Cdd:NF040786   2 NLKQLEAFVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLyeyakemldlWEKLEEE 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 880813463  77 LTRLEKLVHGdVFEPQTSDstvrffglVPQvSHLLPKVVAEIRKQAPNMVVDI---DSI 132
Cdd:NF040786  82 FDRYGKESKG-VLRIGAST--------IPG-QYLLPELLKKFKEKYPNVRFKLmisDSI 130

helix_turn_helix, Arsenical Resistance Operon Repressor;

                           10        20        30
                   ....*....|....*....|....*....|....
gi 880813463    13 ILKHLLE-EKHVSNTALALDMSQPTVSRSLQKLR 45
Cdd:smart00418   2 ILKLLAEgELCVCELAEILGLSQSTVSHHLKKLR 35

The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 110 LLPKVVAEIRKQAPNMVVDIDSIPKRH-FEPLLSGDAHFVLSTHEPLSSEqnLYRMFVISRDYRLLMSKDHPLADKEITV 188
Cdd:cd08417   14 LLPPLLARLRQEAPGVRLRFVPLDRDDlEEALESGEIDLAIGVFPELPPG--LRSQPLFEDRFVCVARKDHPLAGGPLTL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 189 DDLLNSQLGQISLQGDKKLSIESRFKDLGLidkQRQlsIPIQLSNFNVAPDMAEATDIIFHLPTPFAQQAAKQRDLVCKR 268
Cdd:cd08417   92 EDYLAAPHVLVSPRGRGHGLVDDALAELGL---SRR--VALTVPHFLAAPALVAGTDLIATVPRRLAEALAERLGLRVLP 166

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 880813463 269 VPKALrhPSEDVYLYWHKRFHNDPMCRWVRNIFKEL 304
Cdd:cd08417  167 LPFEL--PPFTVSLYWHPRRDRDPAHRWLRELIAEL 200

The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). 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 880813463 110 LLPKVVAEIRKQAPNMVVDIDSIPKRH-FEPLLSGDAHFVLSTHEPLssEQNLYRMFVISRDYRLLMSKDHPLADKEITV 188
Cdd:cd08459   14 FLPRLLAALREVAPGVRIETVRLPVDElEEALESGEIDLAIGYLPDL--GAGFFQQRLFRERYVCLVRKDHPRIGSTLTL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 189 DDLLNSQLGQISLQGDKKLSIESRFKDLGLIDKQRqlsipIQLSNFNVAPDMAEATDIIFHLPTPFAQQAAKQRDLVCKR 268
Cdd:cd08459   92 EQFLAARHVVVSASGTGHGLVEQALREAGIRRRIA-----LRVPHFLALPLIVAQTDLVATVPERLARLFARAGGLRIVP 166

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 880813463 269 VPKALrhPSEDVYLYWHKRFHNDPMCRWVRNIFKEL 304
Cdd:cd08459  167 LPFPL--PPFEVKLYWHRRFHRDPGNRWLRQLVAEL 200

HTH-type transcriptional regulator YidZ;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463   3 LAQVDLNLLVILKHLLEEKHVSNTALALDMSQPTVSRSLQKLRTVFNDDLLVRAAYGYELTPKAEAIKQDLNSVLTR--- 79
Cdd:PRK10216   5 LTTLDLNLLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTPLMVSMEQNLAEWMQMgnq 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463  80 -LEKLVH----GDVFE--PQTSDSTVRFFGLVPQVSHLLPKVVAEIRKQapnmvvDIDSIpkrhfEPLLSGDAHFVLSTH 152
Cdd:PRK10216  85 lLDKPHHqtprGLKFElaAESPLMMIMLNALSKRIYQRYPQATIKLRNW------DYDSL-----DAITRGEVDIGFTGR 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 153 EPLSSEQNLYRMFVISRDYRLLMS--------KDHPLADKEITVDDLLNSQLGQISLQGDKKLSIESRFKDLGlidkqRQ 224
Cdd:PRK10216 154 ESHPRSRELLSLLPLAIDFEVLFSdlpcvwlrKDHPALHEEWNLDTFLRYPHISICWEQSDTWALDDVLQELG-----RE 228

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 225 LSIPIQLSNFNVAPDMAEATDIIFHLPTP-FAQQAAK--QRDLVCKRVP------KALRHPsedVYLYWHKRFHNDPMCR 295
Cdd:PRK10216 229 RTIALSLPEFEQSLFMAAQPDHLLLATAPrYCQYYNQlhQLPLVALPLPfdesqqKKLEVP---FTLLWHKRNSHNPKIV 305

                        330
                 ....*....|
gi 880813463 296 WVRNIFKELY 305
Cdd:PRK10216 306 WLRETIKNLY 315

The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse model of Salmonella. In Vibrio cholerae, LeuO is involved in control of biofilm formation and in the stringent response. The 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 880813463 110 LLPKVVAEIRKQAPNMVVDIDSIPKRH-FEPLLSGDAHFVLSTHEPlsSEQNLYRMFVISRDYRLLMSKDHPLADKEITV 188
Cdd:cd08466   14 LLPRLLARLKQLAPNISLRESPSSEEDlFEDLRLQEVDLVIDYVPF--RDPSFKSELLFEDELVCVARKDHPRIQGSLSL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 189 DDLLNSQlgQISLQGDK-KLSIESRFKDLGLIdkQRQLSIpIQLSNFNVAPdMAEATDIIFHLPTPFAQQAAKQRDLVCK 267
Cdd:cd08466   92 EQYLAEK--HVVLSLRRgNLSALDLLTEEVLP--QRNIAY-EVSSLLSMLA-VVSQTDLIAIAPRWLADQYAEQLNLQIL 165

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 880813463 268 RVPKALRhpSEDVYLYWHKRFHNDPMCRWVRNIFKEL 304
Cdd:cd08466  166 PLPFKTK--PIPLYMVWHKSRERDPAHQWLREQIKQL 200

The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold; Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 110 LLPKVVAEIRKQAPNMVVDIDSI-PKRHFEPLLSGDAHFVLSTHEPlsSEQNLYRMFVISRDYRLLMSKDHPLADKEITV 188
Cdd:cd08467   14 LLPRLAPRLRERAPGLDLRLCPIgDDLAERGLEQGTIDLAVGRFAV--PPDGLVVRRLYDDGFACLVRHGHPALAQEWTL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 189 DDLLNSQLGQISLQGDKKLSIESRFKDLGLIDKqrqlsIPIQLSNFNVAPDMAEATDIIFHLPTPFAQQAAKQRDLVCKR 268
Cdd:cd08467   92 DDFATLRHVAIAPPGRLFGGIYKRLENLGLKRN-----VAIAVSSFLTAAATVAATDLIATVPRRVATQVAAMLPLRVVP 166

                        170       180       190
                 ....*....|....*....|....*....|
gi 880813463 269 VPKALRhpSEDVYLYWHKRFHNDPMCRWVR 298
Cdd:cd08467  167 PPVDLG--TFPVMLIWHERYQHDPAHRWLR 194

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 111 LPKVVAEIRKQAPNMVVDIDSIPKR--HFEPLLSGDAHFVLStHEPLSSEQnLYRMFVISRDYRLLMSKDHPLADKE-IT 187
Cdd:cd08463   15 LPELVARFRREAPGARLEIHPLGPDfdYERALASGELDLVIG-NWPEPPEH-LHLSPLFSDEIVCLMRADHPLARRGlMT 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 188 VDDLLN-SQLGQISLQGDKKLSIESRFKDLGLidKQRqlsIPIQLSNFNVAPDMAEATDIIFHLPTPFAQQAAKQRDLVC 266
Cdd:cd08463   93 LDDYLEaPHLAPTPYSVGQRGVIDSHLARLGL--KRN---IVVTVPYFGLAPYMLAQSDLVFTTGRHFAEHYAKLLPLAV 167

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 880813463 267 KRVPKALrhPSEDVYLYWHKRFHNDPMCRWVRNIFKE 303
Cdd:cd08463  168 VDAPIEF--PRMRYYQLWHERSHRSPEHRWLRRLVAS 202

Bacterial regulatory helix-turn-helix protein, lysR family;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463    8 LNLLVILKHLLEEKHVSNTALALDMSQPTVSRSLQKLRTVFNDDLLVRAAYGYELTPKAE 67
Cdd:pfam00126   1 LRQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 107 VSHLLPKVVAEIRKQAPNMVV------DIDSipkrhfEPLLSGDAHFVLSTHEPLSSE---QNLYR-MFVIsrdyrlLMS 176
Cdd:cd08460   11 VAAFGPALLAAVAAEAPGVRLrfvpesDKDV------DALREGRIDLEIGVLGPTGPEirvQTLFRdRFVG------VVR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 177 KDHPLADKEITVDDLLNSQLGQISLQGDKKLSIESRFKDLGLidkQRQ--LSIPiqlsNFNVAPDMAEATDIIFHLPTPF 254
Cdd:cd08460   79 AGHPLARGPITPERYAAAPHVSVSRRGRLHGPIDDALAALGL---TRRvvAVVP----TFAAALFLARGSDLIALVPERV 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 880813463 255 AQQAAKQRDLVCKRVPKALrhPSEDVYLYWHKRFHNDPMCRWVRNIFKEL 304
Cdd:cd08460  152 TAAARAGLGLRTFPLPLEL--PAVTVSQAWHPRFDADPAHRWLRECVREV 199

The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold; LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. The 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 880813463 110 LLPKVVAEIRKQAPNMVVDIDSIPKR-HFEPLLSGDAHFVLSTHEPLSSEQNLYRMFV-ISRDYRLLMSKDHPLAdKEIT 187
Cdd:cd08468   14 VMPRLMARLEELAPSVRLNLVHAEQKlPLDALLAGEIDFALGYSHDDGAEPRLIEERDwWEDTYVVIASRDHPRL-SRLT 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 188 VDDLLNSQLGQISLQGDKKLSIESRFKDLGLidkqrQLSIPIQLSNFNVAPDMAEATDIIFHLPTPFAQqaAKQRDLVCK 267
Cdd:cd08468   93 LDAFLAERHLVVTPWNEDRGVVDQVLEKQGL-----EREIALQLPNVLNAPFIVASSDLLMTLPRQAAR--ALAEALPLE 165

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 880813463 268 RVPKALRHPSEDVYLYWHKRFHNDPMCRWVRNIFKEL 304
Cdd:cd08468  166 LFDLPFDMPPYRLKLYSHRQHENSAANQWLIEQLDGL 202

transcriptional regulator CysB-like protein; Reviewed

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463   1 MNLAQVDLNLLVILKHLleekHVSNTALALDMSQPTVSRSLQKLRTVFNDDLLVRAAY--------GYELTPKAEAIKQD 72
Cdd:PRK12682   1 MNLQQLRFVREAVRRNL----NLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHGKrlkgltepGKAVLDVIERILRE 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463  73 LNsvltRLEKLvhGDVFEPQTSdSTVRFFGLVPQVSHLLPKVVAEIRKQAPNMVVDI-DSIPKRHFEPLLSGDAHFVLST 151
Cdd:PRK12682  77 VG----NIKRI--GDDFSNQDS-GTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLhQGSPDEIARMVISGEADIGIAT 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 880813463 152 hEPLSSEQNLYRMFVISRDYRLLMSKDHPLADKE-ITVDDL 191
Cdd:PRK12682 150 -ESLADDPDLATLPCYDWQHAVIVPPDHPLAQEErITLEDL 189

DNA-binding transcriptional regulator HcaR; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463  14 LKHL------LEEKHVSNTALALDMSQPTVSRSLQKLRTVFNDDLLVRAAYGYELTPKAEAIKQDLNSVLTRLEKLVhgd 87
Cdd:PRK09906   3 LRHLryfvavAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAEKAK--- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463  88 VFEPQTSDSTVRF-FGLVPQVS-HLLPKVVAEIRKQAPNMVVDIDS-IPKRHFEPLLSGDAHFVLsTHEPLSSEQNLYRm 164
Cdd:PRK09906  80 LRARKIVQEDRQLtIGFVPSAEvNLLPKVLPMFRLRHPDTLIELVSlITTQQEEKLRRGELDVGF-MRHPVYSDEIDYL- 157

                        170       180
                 ....*....|....*....|....*...
gi 880813463 165 FVISRDYRLLMSKDHPLAD-KEITVDDL 191
Cdd:PRK09906 158 ELLDEPLVVVLPVDHPLAHeKEITAAQL 185

The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold; In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. The 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 880813463 111 LPKVVAEIRKQAPNMVVDIDSIPkRH--FEPLLSGDAHFVLSTHEPLSSEQNLYRMFVISrdYRLLMSKDHPLADKEITV 188
Cdd:cd08465   15 LPALMRQLRAEAPGIDLAVSQAS-REamLAQVADGEIDLALGVFPELPEELHAETLFEER--FVCLADRATLPASGGLSL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 189 DDLLNSQLGQISLQGDKKLSIESRFKDLGLidkQRQlsIPIQLSNFNVAPDMAEATDIIFHLPTPFAQQAAKQRDLVCKR 268
Cdd:cd08465   92 DAWLARPHVLVAMRGDAANEIDRALAARGL---RRR--VALTLPHWGVAPELIAGTDLILTVARRALDALRLDERLAVFA 166

                        170       180       190
                 ....*....|....*....|....*....|.
gi 880813463 269 VPKALrhPSEDVYLYWHKRFHNDPMCRWVRN 299
Cdd:cd08465  167 PPFPI--PPFAFQQIWHQRREGDPAHRWLRE 195

The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880813463 110 LLPkVVAEIRKQAPNmvVDIDSIPKRHFEP---LLSGDAHFVLsTHEPLSSEQNLYR-MFvisrDY--RLLMSKDHPLAD 183
Cdd:cd08441   15 LMP-VLDQFRERWPD--VELDLSSGFHFDPlpaLLRGELDLVI-TSDPLPLPGIAYEpLF----DYevVLVVAPDHPLAA 86

                         90
                 ....*....|.
gi 880813463 184 KE-ITVDDLLN 193
Cdd:cd08441   87 KEfITPEDLAD 97

The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is 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 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 880813463 106 QVSHLLPKVVAEIRKQAPNMVVDI-DSIPKRHFEPLLSGDAHFVLSThEPLSSEQNLYRMFVISRDYRLLMSKDHPLADK 184
Cdd:cd08413   10 QARYVLPPVIAAFRKRYPKVKLSLhQGTPSQIAEMVLKGEADIAIAT-EALDDHPDLVTLPCYRWNHCVIVPPGHPLADL 88

                 ....*...
gi 880813463 185 -EITVDDL 191
Cdd:cd08413   89 gPLTLEDL 96

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise 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, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. 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.