Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. 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 family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664327926   1 LKGKKIATPQKGNTQDVAFLNWISEKGwtVDPEsgkGDVSVVRTDNKVTPDAFKQGAVDGAWVPEPTASKLVSDG-GSVL 79
Cdd:cd13553   99 LKGKTIAVPFPGSTHDVLLRYWLAAAG--LDPG---KDVEIVVLPPPDMVAALAAGQIDAYCVGEPWNARAVAEGvGRVL 173

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 664327926  80 LDETTLWPEkkFVITNIIVSQKFLGEHPDVVEAVLKG 116
Cdd:cd13553  174 ADSGDIWPG--HPCCVLVVREDFLEENPEAVQALLKA 208

Substrate binding domain of ABC-type nitrate/bicarbonate transporters, a member of the type 2 periplasmic binding fold superfamily; This subfamily includes nitrate (NrtA) and bicarbonate (CmpA) receptors. These domains are found in eubacterial perisplamic-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding their ligand with high affinity, they 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. These binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664327926   1 LKGKKIATPQKGNTQDVAFLNWISEKGwtVDPEsgkGDVSVVRTDNKVTPDAFKQGAVDGAWVPEPTASKLVSDG-GSVL 79
Cdd:cd13553   99 LKGKTIAVPFPGSTHDVLLRYWLAAAG--LDPG---KDVEIVVLPPPDMVAALAAGQIDAYCVGEPWNARAVAEGvGRVL 173

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 664327926  80 LDETTLWPEkkFVITNIIVSQKFLGEHPDVVEAVLKG 116
Cdd:cd13553  174 ADSGDIWPG--HPCCVLVVREDFLEENPEAVQALLKA 208

NMT1-like family; This family is closely related to the pfam09084 family.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664327926    2 KGKKIATPQKGNTQDVAFLNWISEKGwtVDPESgkgDVSVVRTDNKVTPDAFKQGAVDGAWVPEPTASKLVSDG-GSVLL 80
Cdd:pfam13379 123 KPFKFAVTFPGSTHDLWLRYWLAAGG--LDPDA---DVKLVVVPPPQMVANLRAGNIDGFCVGEPWNARAVAEGiGVTAA 197

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 664327926   81 DETTLW---PEKKFVitniiVSQKFLGEHPDVVEAVLKG 116
Cdd:pfam13379 198 TTGELWkdhPEKVLG-----VRADWVDKNPNAARALVKA 231

taurine transporter substrate binding subunit; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664327926   1 LKGKKIATPQKGNTQdvaFLNWISEKGWTVDPesgkGDVSVVRTDNKVTPDAFKQGAVDGAWVPEPTASKLVSDgGSVLL 80
Cdd:PRK11480 120 LIGKRIAVPFISTTH---YSLLAALKHWGIKP----GQVEIVNLQPPAIIAAWQRGDIDGAYVWAPAVNALEKD-GKVLT 191

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 664327926  81 DETTLWPEKKFVITNIIVSQKFLGEHPDVVEAVLK 115
Cdd:PRK11480 192 DSEQVGQWGAPTLDVWVVRKDFAEKHPEVVKAFAK 226

Substrate binding domain of ABC-type nitrate/bicarbonate transporters, a member of the type 2 periplasmic binding fold superfamily; This subfamily includes nitrate (NrtA) and bicarbonate (CmpA) receptors. These domains are found in eubacterial perisplamic-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding their ligand with high affinity, they 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. These binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664327926   1 LKGKKIATPQKGNTQDVAFLNWISEKGwtVDPEsgkGDVSVVRTDNKVTPDAFKQGAVDGAWVPEPTASKLVSDG-GSVL 79
Cdd:cd13553   99 LKGKTIAVPFPGSTHDVLLRYWLAAAG--LDPG---KDVEIVVLPPPDMVAALAAGQIDAYCVGEPWNARAVAEGvGRVL 173

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 664327926  80 LDETTLWPEkkFVITNIIVSQKFLGEHPDVVEAVLKG 116
Cdd:cd13553  174 ADSGDIWPG--HPCCVLVVREDFLEENPEAVQALLKA 208

Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of the type 2 periplasmic binding fold superfamily; This family represents the periplasmic binding proteins involved in nitrate, alkanesulfonate, and bicarbonate transport. These domains are found in eubacterial perisplamic-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates. Other closest homologs involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB) are also included in this family. After binding their ligand with high affinity, they 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. These binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664327926   1 LKGKKIATPqKGNTQDVAFLNWISEKGWTVDpesgkgDVSVVRTDNKVTPDAFKQGAVDGAWVPEPTASKLVSDG-GSVL 79
Cdd:cd01008  102 LKGKKIAVT-KGTTGHFLLLKALAKAGLSVD------DVELVNLGPADAAAALASGDVDAWVTWEPFLSLAEKGGdARII 174

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 664327926  80 LDETTLWPEkkfVITNIIVSQKFLGEHPDVVEAVLK 115
Cdd:cd01008  175 VDGGGLPYT---DPSVLVARRDFVEENPEAVKALLK 207

ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664327926   1 LKGKKIATPqKGNTQDVAFLNWISEkgWTVDPEsgkgDVSVVrtdNKVTPD---AFKQGAVDGAWVPEPTASKLVSDgGS 77
Cdd:COG4521  127 LKGKKIAVP-FGSTSHYSLLAALKH--AGIDPS----DVTIL---NMQPPEiaaAWQRGDIDAAYVWDPALSELKKS-GK 195

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 664327926  78 VLLDETTLwpEKKFVIT--NIIVSQKFLGEHPDVVEAVLK 115
Cdd:COG4521  196 VLITSAEL--AKWGAPTfdVWVVRKDFAEENPDFVAAFLK 233

Taurine-binding periplasmic protein; the type 2 periplasmic binding protein fold; This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts 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. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664327926   1 LKGKKIATPqKGNTQDVAFLNWIseKGWTVDPesgkGDVSVVrtdNKVTPD---AFKQGAVDGAWVPEPTASKLVSDgGS 77
Cdd:cd13560   99 LAGKKVAVP-FGSTAHYSLLAAL--KHAGVDP----GKVKIL---DMQPPEivaAWQRGDIDAAYVWEPALSQLKKN-GK 167

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 664327926  78 VLLDETTLwpEKKFVIT--NIIVSQKFLGEHPDVVEAVLK 115
Cdd:cd13560  168 VLLSSKDL--AKKGILTfdVWVVRKDFAEKYPDVVAAFLK 205

Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic binding protein fold; This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts 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. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664327926   1 LKGKKIATPQkGNTQDVAFLNWISEKGWTvdpesgKGDVSVVRTDNKVTPDAFKQGAVDGA--WVPEPTASKLVSDGGSV 78
Cdd:cd13561   99 LKGKKIGTPS-GTTADVALDLALRKAGLS------EKDVQIVNMDPAEIVTAFTSGSVDAAalWAPNTATIKEKVPGAVE 171

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 664327926  79 LLDETTLWPEKKFVITnIIVSQKFLGEHPDVVEAVLKG 116
Cdd:cd13561  172 LADNSDFGPDAAVPGA-WVARNKYAEENPEELKKFLAA 208

Putative substrate binding domain of sulfonate binding protein-like, a member of the type 2 periplasmic binding protein fold; This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts 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. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664327926   1 LKGKKIATpQKGNTQDVAFLNWISEKGWTVDpesgkgDVSVVRTDNKVTPDAFKQGAVDGAWVPEPTASKLVSDGGSVLL 80
Cdd:cd13563   98 LKGKTVAV-EEGSVSHFLLLNALEKAGLTEK------DVKIVNMTAGDAGAAFIAGQVDAAVTWEPWLSNALKRGKGKVL 170

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 664327926  81 DETTLWPEkkfVITNIIV-SQKFLGEHPDVVEAVLKG 116
Cdd:cd13563  171 VSSADTPG---LIPDVLVvREDFIKKNPEAVKAVVKA 204

Substrate binding domain of sulfonate binding protein, a member of the type 2 periplasmic binding fold superfamily; This subfamily includes the sulfonate binding domains SsuA found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts 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. The SsuA proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664327926   1 LKGKKIATPQKGNTQDVAfLNWISEKGWTVDpesgkgDVSVVRTDNKVTPDAFKQGAVDgAWVP-EP-TASKLVSDGGSV 78
Cdd:cd13557  101 LKGKKIAFQKGSSAHYLL-VKALEKAGLTLD------DIEPVYLSPADARAAFEQGQVD-AWAIwDPyLAAAELTGGARV 172

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 664327926  79 LLDETTLWPEKKFvitnIIVSQKFLGEHPDVVEAVL 114
Cdd:cd13557  173 LADGEGLVNNRSF----YLAARDFAKDNPEAIQIVL 204

Substrate binding domain of TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold; This group includes Thermus thermophilus GluBP (TtGluBP) of TAXI-TRAP family and closely related proteins. TRAP transporters are ubiquitous in prokaryotes, but absent from eukaryotes. They are comprised of an SBP (substrate-binding protein) of the DctP or TAXI families and two unequally sized integral membrane components. Although TtGluBP is predicted to be an L-glutamate and/or an L-glutamine-binding protein, the substrate spectrum of TAXI proteins remains to be defined. A sequence-homology search also shows that TtGluBP shares low sequence homology with putative immunogenic proteins of uncharacterized function. The substrate-binding domain of TAXI proteins belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and 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 tworeceptor 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 664327926   1 LKGKKIATPQKGNTQDVAFLNWISEKGWTVDpesgkgDVSVVRTDNKVTPDAFKQGAVDGAW----VPEPTASKLVSDGG 76
Cdd:cd13520  108 LKGKRVAVGPPGSGTELTARRLLEAYGLTDD------DVKAEYLGLSDAADALKDGQIDAFFwvggLPASAITELAATRD 181

                 ....*
gi 664327926  77 SVLLD 81
Cdd:cd13520  182 IRLLP 186

NMT1/THI5 like; This family contains the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine.3]. They are regulated by thiamine. The protein adopts a fold related to the periplasmic binding protein (PBP) family. Both pyridoxal-5'-phosphate (PLP) and an iron atom are bound to the protein suggesting numerous residues of the active site necessary for HMP-P biosynthesis. The yeast protein is a dimer and, although exceptionally using PLP as a substrate, has notable similarities with enzymes dependent on this molecule as a cofactor.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664327926    1 LKGKKIATPqkGNTQDVAFLNWISEKGwTVDPEsgkgDVSVVRTDNKVTPDAFKQGAVDGAWVP----EP-TASKLVSDG 75
Cdd:pfam09084  91 LKGKRIGYS--GSPFEEALLKALLKKD-GGDPD----DVTIVNVGGMNLFPALLTGKVDAAIGGyynwEGvELKLEGVEL 163

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 664327926   76 GSVLLDEttlWPEKKFVITNIIVSQKFLGEHPDVVEAVLK 115
Cdd:pfam09084 164 NIFALAD---YGVPDYYSLVLITNEAFLKENPELVRAFLR 200

Substrate binding domain of 2'-hydroxybiphenyl-2-sulfinate desulfinase, a member of the type 2 periplasmic binding fold superfamily; This subfamily includes DszB, which converts 2'-hydroxybiphenyl-2-sulfinate to 2-hydroxybiphenyl and sulfinate at the rate-limiting step of the microbial dibenzothiophene desulfurization pathway. The overall fold of DszB is highly similar to those of periplasmic substrate-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates. After binding their ligand with high affinity, they 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. The DszB protein belongs to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664327926   1 LKGKKIATPQ---KGNTQDVAFLNWISEKGWTVDpesgkgdvsVVRTDNKVT--PDAFKQGAVDGAWVPEPTASKLVSDG 75
Cdd:cd13554  102 LEGKRIGMSAgaiRGSWLARALLHNLEIGGLDVE---------IVPIDSPGRgqAAALDSGDIDALASWLPWATTLQATG 172

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 664327926  76 GSVLLDETTLWPeKKFVITNIIVSQKFLGEHPDVVEAVLKG 116
Cdd:cd13554  173 GARPLVDLGLVE-GNSYYSTWTVRSDFIEQNPEAVKALVEA 212