PBP superfamily domain; This family belongs to the periplasmic binding domain superfamily. It is often associated with a helix-turn-helix domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738078799  146 VDIKYRESVEAVKALARGECDMAGFHLPRGAFRANCAQIYRPWLDDTRHVLIHLTRRKQGLFIPRGNPKGVVGLADLARE 225
Cdd:pfam12727  13 LAVAYVGSLGGLAALRRGEAHIAGIHLLDPETGEYNLPFLRRLLPGIPVVLINLAYREQGLVVAPGNPKGITGWEDLARP 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738078799  226 DVRFVNRQPGSGTRMLLDLALREIGVDPERINGYASAELTHSAIAAFVASGMADLGFGVEPAAHHF-GLAFIPVVDEDYY 304
Cdd:pfam12727  93 GLRFVNRQRGSGTRVLLDELLRKAGIDPSDINGYDREERSHLAVAAAVASGRADAGLGIEAAARALgGLDFIPLARERYD 172

                         170       180
                  ....*....|....*....|
gi 738078799  305 FACEQGRLGDPPLAGALSLL 324
Cdd:pfam12727 173 LVIPKEALDDPAVQALLEVL 192

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. 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 738078799 122 LRIHASH---GYAVAALVSALVDGHAQVDIKYRE--SVEAVKALARGECDMA--GFHLPRGAFrancaqIYRPWLDDtRH 194
Cdd:cd08420    2 LRIGASTtigEYLLPRLLARFRKRYPEVRVSLTIgnTEEIAERVLDGEIDLGlvEGPVDHPDL------IVEPFAED-EL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738078799 195 VLIhltrrkqglfIPRGNP---KGVVGLADLAREdvRFVNRQPGSGTRMLLDLALREIGVDPERINgyASAELTHS-AIA 270
Cdd:cd08420   75 VLV----------VPPDHPlagRKEVTAEELAAE--PWILREPGSGTREVFERALAEAGLDGLDLN--IVMELGSTeAIK 140

                 ....*..
gi 738078799 271 AFVASGM 277
Cdd:cd08420  141 EAVEAGL 147

PBP superfamily domain; This family belongs to the periplasmic binding domain superfamily. It is often associated with a helix-turn-helix domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738078799  146 VDIKYRESVEAVKALARGECDMAGFHLPRGAFRANCAQIYRPWLDDTRHVLIHLTRRKQGLFIPRGNPKGVVGLADLARE 225
Cdd:pfam12727  13 LAVAYVGSLGGLAALRRGEAHIAGIHLLDPETGEYNLPFLRRLLPGIPVVLINLAYREQGLVVAPGNPKGITGWEDLARP 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738078799  226 DVRFVNRQPGSGTRMLLDLALREIGVDPERINGYASAELTHSAIAAFVASGMADLGFGVEPAAHHF-GLAFIPVVDEDYY 304
Cdd:pfam12727  93 GLRFVNRQRGSGTRVLLDELLRKAGIDPSDINGYDREERSHLAVAAAVASGRADAGLGIEAAARALgGLDFIPLARERYD 172

                         170       180
                  ....*....|....*....|
gi 738078799  305 FACEQGRLGDPPLAGALSLL 324
Cdd:pfam12727 173 LVIPKEALDDPAVQALLEVL 192

DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738078799  28 LLELVATTGSIAQAAEAKGLSYRHAWGLLRALEACVGGALIETARGK----GTSLSELGAAVIGAQRLVGERLGGNLRAL 103
Cdd:COG2005   26 LLEAIDETGSISAAAKAMGMSYKRAWDLIDAMNNLLGEPLVERQTGGkgggGARLTPEGRRLLALYRRLEAEAQRALAAL 105

                         90
                 ....*....|.
gi 738078799 104 AAEVASELNRR 114
Cdd:COG2005  106 FEELFALLRSK 116

ModE molybdate transport repressor domain; ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins. [Regulatory functions, Other]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 738078799   26 VPLLELVATTGSIAQAAEAKGLSYRHAWGLLRALEACVGGALIETARGK----GTSLSELGAAVI 86
Cdd:TIGR00637   7 VALLKAIARMGSISQAAKDAGISYKSAWDYIRAMNNLSGEPLVERATGGkgggGAVLTEYGQRLI 71

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 738078799 122 LRIHASH---GYAVAALVSALVDGHAQVDIKYRE--SVEAVKALARGECDMAGFHLPrgafrancaqiyrpwLDDTRHVL 196
Cdd:cd05466    2 LRIGASPsiaAYLLPPLLAAFRQRYPGVELSLVEggSSELLEALLEGELDLAIVALP---------------VDDPGLES 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738078799 197 IHLTRRKQGLFIPRGNP---KGVVGLADLAREdvRFVNRQPGSGTRMLLDLALREIGVDPERIngyasAELTH-SAIAAF 272
Cdd:cd05466   67 EPLFEEPLVLVVPPDHPlakRKSVTLADLADE--PLILFERGSGLRRLLDRAFAEAGFTPNIA-----LEVDSlEAIKAL 139

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 738078799 273 VASGMadlGFGVEPA-----AHHFGLAFIPVVDED 302
Cdd:cd05466  140 VAAGL---GIALLPEsaveeLADGGLVVLPLEDPP 171

DNA-binding transcriptional regulator, LysR family [Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738078799  32 VATTGSIAQAAEAKG-----LSYRhawglLRALEACVGGALIEtaR-GKGTSLSELGAAVIG-AQRLVgerlggnlrALA 104
Cdd:COG0583   12 VAEEGSFTAAAERLGvsqpaVSRQ-----IRRLEEELGVPLFE--RtGRGLRLTEAGERLLErARRIL---------AEL 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 738078799 105 AEVASELNRRLTQHPGALRIHASHGYA---VAALVSALVDGHAQVDIKYRE--SVEAVKALARGECDMA 168
Cdd:COG0583   76 EEAEAELRALRGGPRGTLRIGAPPSLArylLPPLLARFRARHPGVRLELREgnSDRLVDALLEGELDLA 144

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). 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
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 738078799 219 LADLAREdvRFVNRQPGSGTRMLLDLALREIGVDPERINGYASAElthsAIAAFVASGM 277
Cdd:cd08419   91 LERLARE--PFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNE----AIKQAVMAGL 143

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738078799 132 VAALVSALVDGHAQVDIKYRE--SVEAVKALARGECDMA----GFHLPRG-AFRAncaqiyrpwLDDTRHVLIhltrrkq 204
Cdd:cd08436   15 LPELLARFHRRHPGVDIRLRQagSDDLLAAVREGRLDLAfvglPERRPPGlASRE---------LAREPLVAV------- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738078799 205 glfIPRGNP---KGVVGLADLAREDvrFVNRQPGSGTRMLLDLALREIGVDPERingyaSAELTH-SAIAAFVASGmadL 280
Cdd:cd08436   79 ---VAPDHPlagRRRVALADLADEP--FVDFPPGTGARRQVDRAFAAAGVRRRV-----AFEVSDvDLLLDLVARG---L 145

                        170       180
                 ....*....|....*....|....
gi 738078799 281 GFGVEP---AAHHFGLAFIPVVDE 301
Cdd:cd08436  146 GVALLPasvAARLPGLAALPLEPA 169

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738078799 122 LRIHASHGYAVAAL---VSALVDGHAQVDIKY--RESVEAVKALARGECDMaGFHLPRGAFRancaQIYRPWLDDTRHVL 196
Cdd:cd08415    2 LRIAALPALALSLLpraIARFRARHPDVRISLhtLSSSTVVEAVLSGQADL-GLASLPLDHP----GLESEPLASGRAVC 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738078799 197 IhltrrkqglfIPRGNP---KGVVGLADLAREdvRFVNRQPGSGTRMLLDLALREIGVDPERIngyASAELTHSAiAAFV 273
Cdd:cd08415   77 V----------LPPGHPlarKDVVTPADLAGE--PLISLGRGDPLRQRVDAAFERAGVEPRIV---IETQLSHTA-CALV 140

                 ....
gi 738078799 274 ASGM 277
Cdd:cd08415  141 AAGL 144

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738078799 132 VAALVSALVDGHAQVDIKYRE--SVEAVKALARGECDMA-GFHLPRGAFRANCAQIYRPWLDDTRHVLIHLTRRKQGlfi 208
Cdd:cd08423   15 LPPALAALRARHPGLEVRLREaePPESLDALRAGELDLAvVFDYPVTPPPDDPGLTRVPLLDDPLDLVLPADHPLAG--- 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738078799 209 prgnpKGVVGLADLAreDVRFVNRQPGSGTRMLLDLALREIGVDPE---RINGYAsaelthsAIAAFVASGmadLGFGVE 285
Cdd:cd08423   92 -----REEVALADLA--DEPWIAGCPGSPCHRWLVRACRAAGFTPRiahEADDYA-------TVLALVAAG---LGVALV 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 738078799 286 PA----AHHFGLAFIPVVDED--YYFACEQGRLGDPPLAGAL 321
Cdd:cd08423  155 PRlalgARPPGVVVRPLRPPPtrRIYAAVRAGAARRPAVAAA 196

Ligand-binding domain of a glycoprotein adhesion and an accessory colonization factor, a member of the type 2 periplasmic binding fold superfamily; PEB3 is a glycoprotein adhesion from Campylobacter jejuni whose structure suggests a functional role in transport, and resembles PEB1a, an Asp/Glu transporter and an adhesin. The overall structure of PEB3 is a dimer and is similar to that of other type 2 periplasmic transport proteins such as the molybdate/tungstate, sulfate, and ferric iron transporters. PEB3 has high sequence identity to Paa, an Escherichia coli adhesin, and to AcfC, an accessory colonization factor from Vibrio cholera.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738078799 199 LTRRKQGLFIPRGNPKGVVGLADLAREDVRFVNRQPGSGTRMLLDLALRE---IGVDPERINGYASAELTHSAIAAFVAS 275
Cdd:cd13519   77 LYLRPSAILVRKGNPKKIKGLKDLLKPGVKILVVNGAGQTGLWEDMAGRTgdiETVRAFRKNIVVFAKNSGAARKAWKQD 156

                 ....
gi 738078799 276 GMAD 279
Cdd:cd13519  157 PNID 160