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 504968989 154 GQADFLVTTLDQFLKQKPQG---KIVGLINYTIGGDAVVLnTKQYPNLRSLQALNQLVQQrrsqnqlsiifagDSPSEYL 230
Cdd:cd13563   49 GQIDAAATTLDDALAMAAKGvpvKIVLVLDNSNGADGIVA-KPGIKSIADLKGKTVAVEE-------------GSVSHFL 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504968989 231 glLLDAKFEAFrlLDFQTIKVV-----DAADAWkqlQSNsNLAAAILWEPFVTKARQQGYTVVL-SSRDTPGAIVDVIVA 304
Cdd:cd13563  115 --LLNALEKAG--LTEKDVKIVnmtagDAGAAF---IAG-QVDAAVTWEPWLSNALKRGKGKVLvSSADTPGLIPDVLVV 186

                        170       180
                 ....*....|....*....|.
gi 504968989 305 GDRLLQSQPEKISAFLEAYYR 325
Cdd:cd13563  187 REDFIKKNPEAVKAVVKAWFD 207

Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; OmpA-like domains (named after the C-terminal domain of Escherichia coli OmpA protein) have been shown to non-covalently associate with peptidoglycan, a network of glycan chains composed of disaccharides, which are crosslinked via short peptide bridges. Well-studied members of this family include the Escherichia coli outer membrane protein OmpA, the Escherichia coli lipoprotein PAL, Neisseria meningitdis RmpM, which interact with the outer membrane, as well as the Escherichia coli motor protein MotB, and the Vibrio flagellar motor proteins PomB and MotY, which interact with the inner membrane.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504968989 461 IEFQFGSTTLTRKGKQTLDRLAKQIAEFNSQTvaIRVIGHTSRKGLADLNQKLSQQRAQEVINYLKQRGL-QHKMFAVGK 539
Cdd:cd07185    4 IYFDFGSAELTPEAKPLLDKLAEVLKKNPDAK--IRIEGHTDSRGSDAYNQELSERRAEAVADYLVSKGVdASRITAVGY 81

                         90       100
                 ....*....|....*....|....*
gi 504968989 540 GFSQLRGDISPYDNR--NQRTEIQL 562
Cdd:cd07185   82 GESRPIASNDTEEGRakNRRVEIVI 106

OmpA family; The Pfam entry also includes MotB and related proteins which are not included in the Prosite family.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504968989  463 FQFGSTTLTRKGKQTLDRLAKQIaEFNSQTVAIRVIGHTSRKGLADLNQKLSQQRAQEVINYLKQRGLQHK-MFAVGKG 540
Cdd:pfam00691   1 FDPGSSQLTPKAKATLDEIADLL-KFPELKNTITIEGHTDTVGSAAYNWELSQRRAEAVRRYLVNFGVPPSrISVVGYG 78

outer membrane protein A; Reviewed

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504968989 463 FQFGSTTLTRKGKQTLDRLAKQIAEFNSQTVAIRVIGHTSRKGLADLNQKLSQQRAQEVINYLKQRGL-QHKMFAVGKG 540
Cdd:PRK10808 228 FNFNKATLKPEGQQALDQLYSQLSNLDPKDGSVVVLGYTDRIGSDAYNQGLSEKRAQSVVDYLVSKGIpADKISARGMG 306

Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; OmpA-like domains (named after the C-terminal domain of Escherichia coli OmpA protein) have been shown to non-covalently associate with peptidoglycan, a network of glycan chains composed of disaccharides, which are crosslinked via short peptide bridges. Well-studied members of this family include the Escherichia coli outer membrane protein OmpA, the Escherichia coli lipoprotein PAL, Neisseria meningitdis RmpM, which interact with the outer membrane, as well as the Escherichia coli motor protein MotB, and the Vibrio flagellar motor proteins PomB and MotY, which interact with the inner membrane.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504968989 461 IEFQFGSTTLTRKGKQTLDRLAKQIAEFNSQTvaIRVIGHTSRKGLADLNQKLSQQRAQEVINYLKQRGL-QHKMFAVGK 539
Cdd:cd07185    4 IYFDFGSAELTPEAKPLLDKLAEVLKKNPDAK--IRIEGHTDSRGSDAYNQELSERRAEAVADYLVSKGVdASRITAVGY 81

                         90       100
                 ....*....|....*....|....*
gi 504968989 540 GFSQLRGDISPYDNR--NQRTEIQL 562
Cdd:cd07185   82 GESRPIASNDTEEGRakNRRVEIVI 106

OmpA family; The Pfam entry also includes MotB and related proteins which are not included in the Prosite family.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504968989  463 FQFGSTTLTRKGKQTLDRLAKQIaEFNSQTVAIRVIGHTSRKGLADLNQKLSQQRAQEVINYLKQRGLQHK-MFAVGKG 540
Cdd:pfam00691   1 FDPGSSQLTPKAKATLDEIADLL-KFPELKNTITIEGHTDTVGSAAYNWELSQRRAEAVRRYLVNFGVPPSrISVVGYG 78

ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion transport and metabolism];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504968989 150 LLNEGQADFLVTTLDQFLKQKPQG---KIVGLINYTiGGDAVVLNTKqyPNLRSLQALnqlvQQRRsqnqlsIIFAGDSP 226
Cdd:COG0715   67 ALAAGQADFGVAGAPPALAARAKGapvKAVAALSQS-GGNALVVRKD--SGIKSLADL----KGKK------VAVPGGST 133

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504968989 227 SEYL--GLLLDAKfeafrlLDFQTIKVV--DAADAWKQLQSNsNLAAAILWEPFVTKARQQG-YTVVLSSRD-TPGAIVD 300
Cdd:COG0715  134 SHYLlrALLAKAG------LDPKDVEIVnlPPPDAVAALLAG-QVDAAVVWEPFESQAEKKGgGRVLADSADlVPGYPGD 206

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 504968989 301 VIVAGDRLLQSQPEKISAFLEAYYRLIDTSTSDRLLLQNQIARDGNLSASDATTVMQG 358
Cdd:COG0715  207 VLVASEDFLEENPEAVKAFLRALLKAWAWAAANPDEAAAILAKATGLDPEVLAAALEG 264

Putative substrate binding domain of an ABC-type transporter similar to ThiY/THI5; the type 2 periplasmic binding protein fold; This subfamily is phylogenetically similar to ThiY, which is the periplasmic N-formyl-4-amino-5-(aminomethyl)-2-methylpyrimidine (FAMP) binding component of the ABC transport system (ThiXYZ). FAMP is imported into cell by the transporter, where it is then incorporated into the thiamin biosynthetic pathway. The closest structural homologs of ThiY are THI5, which is responsible for the synthesis of 4-amino-5-(hydroxymethyl)-2-methylpyrimidine phosphate (HMP-P) in the thiamin biosynthetic pathway of eukaryotes, and periplasmic binding proteins involved in alkanesulfonate/nitrate and bicarbonate transport. After binding the ligand, 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 ThiY/THI5 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504968989 264 NSNLAAAILWEPFVTKARQQGYTVVLSSRDTPGA--IVDVIVAGDRlLQSQPEKISAFLEAY 323
Cdd:cd13652  154 NGNVDAAVLAEPFLSRARSSGAKVVASDYADPDPhsQATMVFSADF-ARENPEVVKKFLRAY 214

Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic binding protein fold; This subfamily includes sulfonate binding domains 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504968989 264 NSNLAAAILWEPFVTKARQQGYTVVLssRDTPG--AIVDVIVAGDRLLQSQPEKISAFLEAYYR 325
Cdd:cd13562  153 NGDIDAAVIWEPLITKLLSDGVVRVL--RDGTGikDGLNVIVARGPLIEQNPEVVKALLKAYQR 214

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504968989 248 TIKVVDAADAWKQLQSNsNLAAAILWEPFVTKARQQGY-TVVLSSRDT-PGAIVDVIVAGDRLLQSQPEKISAFLEAY 323
Cdd:cd13553  133 EIVVLPPPDMVAALAAG-QIDAYCVGEPWNARAVAEGVgRVLADSGDIwPGHPCCVLVVREDFLEENPEAVQALLKAL 209

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 504968989 222 AGDSPSEYLGLLLdaKFEAFRLLDFQTIKVvDAADAWKQLQSNSnLAAAILWEPFVTKARQQGY-TVVLSSRDTPG---A 297
Cdd:cd13561  108 SGTTADVALDLAL--RKAGLSEKDVQIVNM-DPAEIVTAFTSGS-VDAAALWAPNTATIKEKVPgAVELADNSDFGpdaA 183

                         90       100
                 ....*....|....*....|....*...
gi 504968989 298 IVDVIVAGDRLLQSQPEKISAFLEAYYR 325
Cdd:cd13561  184 VPGAWVARNKYAEENPEELKKFLAALAE 211