Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857   37 TLTI-VYYEQPGLIYKD-NGQMKGVCVDIlsdfAKFIQEKYSKTVTVnyageeREFSGFLKVvqstPNI------LGVTN 108
Cdd:smart00062   1 TLRVgTNGDYPPFSFADeDGELTGFDVDL----AKAIAKELGLKVEF------VEVSFDSLL----TALksgkidVVAAG 66

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857  109 TSITEERKKILKFTPPFMTTQLVLLTNQNSPaLTNLKDLpkvyAGFSALVITGSTHMKYAdmlkKQYYPDLNITYAPSSE 188
Cdd:smart00062  67 MTITPERAKQVDFSDPYYRSGQVILVRKDSP-IKSLEDL----KGKKVAVVAGTTAEELL----KKLYPEAKIVSYDSNA 137

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857  189 TVIKSLtANPKIFSILDFTEYVGVVRKKLPIKRQDV---DLGNAEELGFIMAKqsdWDGLWKEFLTD---DYRKGVRYKK 262
Cdd:smart00062 138 EALAAL-KAGRADAAVADAPLLAALVKQHGLPELKIvpdPLDTPEGYAIAVRK---GDPELLDKINKalkELKADGTLKK 213

                   ..
gi 1482688857  263 II 264
Cdd:smart00062 214 IS 215

Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. This domain recognizes Nicotinate, quidalnate, pyridine-2,5-dicarboxylate and salicylate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857  50 YKDNGQMKGVCVDILSDFAKFIQEKYsKTVTVNyageereFSGFLKVVQStpnilG-----VTNTSITEERKKILKFTPP 124
Cdd:pfam00497  15 VDENGKLVGFDVDLAKAIAKRLGVKV-EFVPVS-------WDGLIPALQS-----GkvdliIAGMTITPERAKQVDFSDP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857 125 FMTTQLVLLTNQNSPA--LTNLKDLpkvyAGFSALVITGSTHMKYADMLKKqyyPDLNITYAPSSETVIKSLTANpKI-F 201
Cdd:pfam00497  82 YYYSGQVILVRKKDSSksIKSLADL----KGKTVGVQKGSTAEELLKNLKL---PGAEIVEYDDDAEALQALANG-RVdA 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1482688857 202 SILDFTEYVGVVRK-KLPIKRQDVDLGNAEELGFIMAKQSD 241
Cdd:pfam00497 154 VVADSPVAAYLIKKnPGLNLVVVGEPLSPEPYGIAVRKGDP 194

Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, Signal transduction mechanisms];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857  18 AGQKYQGNSWADVKAagKGTLTIVYYEQPGLIYKDNGQMKGVCVDILSDFAKFIQEKYSKTVTVNyageereFSGFLKVV 97
Cdd:COG4623     6 PACSSEPGDLEQIKE--RGVLRVLTRNSPTTYFIYRGGPMGFEYELAKAFADYLGVKLEIIVPDN-------LDELLPAL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857  98 QSTPNILGVTNTSITEERKKILKFTPPFMTTQLVLLTNQNSPALTNLKDLpkvyAGFSALVITGSTHMKYADMLKKQyYP 177
Cdd:COG4623    77 NAGEGDIAAAGLTITPERKKQVRFSPPYYSVSQVLVYRKGSPRPKSLEDL----AGKTVHVRAGSSYAERLKQLNQE-GP 151

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1482688857 178 DLNITYAPSSETV-IKSLTANPKI-FSILDFTEyVGVVRKKLPIKRQDVDLGNAEELGFIMAKQSDW 242
Cdd:COG4623   152 PLKWEEDEDLETEdLLEMVAAGEIdYTVADSNI-AALNQRYYPNLRVAFDLSEPQPIAWAVRKNDPS 217

Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1, 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 majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857  50 YKDNGQMKGVCVDILSDFAKfiqeKYSKTVTVnyagEEREFSGFLKVVQSTpNI-LGVTNTSITEERKKILKFTPPFMTT 128
Cdd:cd13530    16 IDKNGKLVGFDVDLANAIAK----RLGVKVEF----VDTDFDGLIPALQSG-KIdVAISGMTITPERAKVVDFSDPYYYT 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857 129 QLVLLTNQNSPALTNLKDLPKVYAGfsalVITGSTHMKYAdmlkKQYYPDLNITYAPSSETVIKSLTANpKI-FSILDFT 207
Cdd:cd13530    87 GQVLVVKKDSKITKTVADLKGKKVG----VQAGTTGEDYA----KKNLPNAEVVTYDNYPEALQALKAG-RIdAVITDAP 157

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1482688857 208 EYVGVVRKKLPIKRQDVDLGNAEELGFIMAKQSD 241
Cdd:cd13530   158 VAKYYVKKNGPDLKVVGEPLTPEPYGIAVRKGNP 191

The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold protein superfamily; This subfamily includes the solute binding domain YfhD_N. These domains are found in the YfhD proteins that are predicted to function as lytic transglycosylases that cleave the glycosidic bond between N-acetylmuramic acid and N-acetylglucosamin in peptidoglycan, while the YfhD_N domain might act as an auxiliary or regulatory subunit. In addition to periplasmic solute binding domain, they have an SLT domain, typically found in soluble lytic transglycosylases, and a C-terminal low complexity domain. The YfhD proteins might have been recruited to create localized cell wall openings required for transport of large substrates such as DNA. They 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 1482688857  50 YKDNGQMKGVCVDILSDFAKFIQEKYskTVTVNYAGEERefsgFLKVVQSTPNILGvTNTSITEERKKILKFTPPFMTTQ 129
Cdd:cd01009    15 YIDRGGPRGFEYELAKAFADYLGVEL--EIVPADNLEEL----LEALEEGKGDLAA-AGLTITPERKKKVDFSFPYYYVV 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857 130 LVLLTNQNSPALTNLKDLpkvyAGFSALVITGSTHMKYADMLKKQyYPDLNITYAPSSETV-IKSLTANPKI-FSILDFT 207
Cdd:cd01009    88 QVLVYRKGSPRPRSLEDL----SGKTIAVRKGSSYAETLQKLNKG-GPPLTWEEVDEALTEeLLEMVAAGEIdYTVADSN 162

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1482688857 208 EYVgVVRKKLPIKRQDVDLGNAEELGFIMAKQSD 241
Cdd:cd01009   163 IAA-LWRRYYPELRVAFDLSEPQPLAWAVRKNSP 195

Glutamine-binding domain of ABC transporter, a member of the type 2 periplasmic binding fold protein superfamily; Periplasmic glutamine binding domain GlnP serves as an initial receptor in the ABC transport of glutamine in eubacteria. GlnP 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 two receptor 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 1482688857  51 KDNGQMKGVCVDILSDFAKfiQEKYskTVTVNYAGeereFSGFLKVVQSTPNILGVTNTSITEERKKILKFTPPFMTTQL 130
Cdd:cd13619    17 NDDGKYVGIDVDLLNAIAK--DQGF--KVELKPMG----FDAAIQAVQSGQADGVIAGMSITDERKKTFDFSDPYYDSGL 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1482688857 131 VLLTNQNSPALTNLKDLpkvyAGFSALVITGSTHMKYADMLKKQYypDLNITYAPSSETVIKSLTAN 197
Cdd:cd13619    89 VIAVKKDNTSIKSYEDL----KGKTVAVKNGTAGATFAESNKEKY--GYTIKYFDDSDSMYQAVENG 149

Putative sensor domain similar to BvgS; the type 2 periplasmic binding protein domain; BvgS is composed of two periplasmic domains homologous to bacterial periplasmic-binding proteins (PBPs), a transmembrane region followed successively by a cytoplasmic PAS (Per/ARNT/SIM), a Histidine-kinase (HK), a receiver and a Histidine phosphotransfer (Hpt) domains. The sensor protein BvgS can autophosphorylate and phosphorylate the response regulator BvgA. The BvgAS phosphorelay controls the expression of virulence factors in response to certain environmental stimuli in Bordetella pertussis. Its close homologs, Escherichia coli EvgS and Klebsiella pneumoniae KvgS, appear to be involved in the transcriptional regulation of drug efflux pumps and in countering free radical stresses and sensing iron limiting conditions, respectively. The periplasmic sensor domain of BvgS 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 two receptor 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 1482688857 112 TEERKKILKFTPPFMTTQLVLLTNQNSPALTNLKDL-------PKVYAgfsalvitgsthmkYADMLkKQYYPDLNITYA 184
Cdd:cd13708    72 TPEREEYLNFTKPYLSDPNVLVTREDHPFIADLSDLgdktigvVKGYA--------------IEEIL-RQKYPNLNIVEV 136

                          90       100
                  ....*....|....*....|.
gi 1482688857 185 PSSETVIKsLTANPKIFSILD 205
Cdd:cd13708   137 DSEEEGLK-KVSNGELFGFID 156

The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding fold protein; This subfamily includes the periplasmic sensor domain of the histidine kinase receptors (HisK) which are elements of the two-component signal transduction systems commonly found in bacteria and lower eukaryotes. Typically, the two-component system consists of a membrane-spanning histidine kinase sensor and a cytoplasmic response regulator. The two-component systems serve as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. Extracellular stimuli such as small molecule ligands and ions are detected by the N-terminal periplasmic sensing domain of the sensor kinase receptor, which regulate the catalytic activity of the cytoplasmic kinase domain and promote ATP-dependent autophosphorylation of a conserved histidine residue. The phosphate is then transferred to a conserved aspartate in the response regulator through a phospho-transfer mechanism, and the activity of the response regulator is in turn regulated. The sensor domain 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 through their function as an initial high-affinity binding component. 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857 106 VTNTSITEERKKILKFTPPFMTTQLVLLTNQNSPALTNLKDLpkvyAGFSALVITGSTHMKYAdmlkKQYYPDLNITYAP 185
Cdd:cd13704    65 LIGMAYSEERAKLFDFSDPYLEVSVSIFVRKGSSIINSLEDL----KGKKVAVQRGDIMHEYL----KERGLGINLVLVD 136

                  ....*....
gi 1482688857 186 SSETVIKSL 194
Cdd:cd13704   137 SPEEALRLL 145

Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein fold; This group includes periplasmic glutamate-binding domain GluB from Corynebacterium efficiens and its related proteins. The GluB domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins 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. 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 receptor 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 1482688857  31 KAAGKGTLTI-VYYEQPGLIYKD--NGQMKGVCVDILSDFAKFIQEKYSKTVTVNYAGEEREfsgflKVVQSTPNILGVT 107
Cdd:cd13690     3 KIRKRGRLRVgVKFDQPGFSLRNptTGEFEGFDVDIARAVARAIGGDEPKVEFREVTSAERE-----ALLQNGTVDLVVA 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857 108 NTSITEERKKILKFTPPFMTTQLVLLTNQNSPALTNLKDLpkvyAGFSALVITGSThmkYADMLKKQYYP 177
Cdd:cd13690    78 TYSITPERRKQVDFAGPYYTAGQRLLVRAGSKIITSPEDL----NGKTVCTAAGST---SADNLKKNAPG 140

Putative sensor domain similar to HisK; the type 2 periplasmic binding fold protein; This group includes periplasmic sensor domain of the histidine kinase receptors (HisK) which are elements of the two-component signal transduction systems commonly found in bacteria and lower eukaryotes. Typically, the two-component system consists of a membrane-spanning histidine kinase sensor and a cytoplasmic response regulator. The two-component systems serve as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. Extracellular stimuli such as small molecule ligands and ions are detected by the N-terminal periplasmic sensing domain of the sensor kinase receptor, which regulate the catalytic activity of the cytoplasmic kinase domain and promote ATP-dependent autophosphorylation of a conserved histidine residue. The phosphate is then transferred to a conserved aspartate in the response regulator through a phospho-transfer mechanism, and the activity of the response regulator is in turn regulated. The sensor domain 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 through their function as an initial high-affinity binding component. 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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857 112 TEERKKILKFTPPFMTTQLVLLTNQNSPALTNLKDLpkvyAGFSALVITGSTHMKYAdmlkKQYYPDLNITYAPSSETVI 191
Cdd:cd13706    71 SPEREKYLDFSQPIATIDTYLYFHKDLSGITNLSDL----KGFRVGVVKGDAEEEFL----RAHGPILSLVYYDNYEAMI 142

                  ....*.
gi 1482688857 192 KSLTAN 197
Cdd:cd13706   143 EAAKAG 148

Substrate-binding domain of putative amino acid-binding protein; the type 2 periplasmic-binding protein fold; This putative amino acid-binding protein 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 two receptor 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 1482688857  50 YKDNGQMKGVCVDILSDFAKFIQEKYSKTVTvnyageerEFSGFLKVVQSTPNILGVTNTSITEERKKILKFTPPFMTTQ 129
Cdd:cd13625    20 FVENGKIVGFDRDLLDEMAKKLGVKVEQQDL--------PWSGILPGLLAGKFDMVATSVTITKERAKRFAFTLPIAEAT 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857 130 LVLLTNQNSPALTNLKDLpkvyAGFSALVITGSTHM----KYADMLKKQY---------YPDLNITYAP----SSETVIK 192
Cdd:cd13625    92 AALLKRAGDDSIKTIEDL----AGKVVGVQAGSAQLaqlkEFNETLKKKGgngfgeikeYVSYPQAYADlangRVDAVAN 167

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1482688857 193 SLT-------ANPKIFSI---LDFTEYVGVVrkklpIKRQDVDLGNA 229
Cdd:cd13625   168 SLTnlaylikQRPGVFALvgpVGGPTYFAWV-----IRKGDAELRKA 209

Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold; This group contains uncharacterized periplasmic cystine-binding domain of ATP-binding cassette (ABC) transporters. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Likewise, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins 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. 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 receptor 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 1482688857  52 DNGQMKGVCVDIlsdfAKFIQEKYSKTVTVnyagEEREFSGFLKVVQSTPNILGVTNTSITEERKKILKFTPPFMTTQLV 131
Cdd:cd13713    18 EDNQLVGFDVDV----AKAIAKRLGVKVEP----VTTAWDGIIAGLWAGRYDIIIGSMTITEERLKVVDFSNPYYYSGAQ 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857 132 LLTNQNSPAlTNLKDLPKVYAGfsalVITGSTHMKYAdmlkKQYYPDLNITYAPSSETVIKSLTANPKIFSILDftEYVG 211
Cdd:cd13713    90 IFVRKDSTI-TSLADLKGKKVG----VVTGTTYEAYA----RKYLPGAEIKTYDSDVLALQDLALGRLDAVITD--RVTG 158

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1482688857 212 VVRKK---LPIKRQDvDLGNAEELGFIMAKQSD 241
Cdd:cd13713   159 LNAIKeggLPIKIVG-KPLYYEPMAIAIRKGDP 190

Substrate binding domain of ABC cysteine transporter; the type 2 periplasmic binding protein fold; This subfamily comprises of the periplasmic-binding protein component of ABC transporter specific for cysteine and its closely related proteins. The cysteine-binding domains belong to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins 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. 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 receptor 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 1482688857  35 KGTLTI-VYYEQPGLIYKD-NGQMKGVCVDILSDFAKFIQEKYSKTVTVNYAGEERefsgfLKVVQSTPNILGVTNTSIT 112
Cdd:cd13694     7 SGVIRIgVFGDKPPFGYVDeNGKFQGFDIDLAKQIAKDLFGSGVKVEFVLVEAANR-----VPYLTSGKVDLILANFTVT 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1482688857 113 EERKKILKFTPPFMTTQLVLLTNQNSPaLTNLKDLpkvyAGFSALVITGSTHMKYadmLKKQyYPDLNITY 183
Cdd:cd13694    82 PERAEVVDFANPYMKVALGVVSPKDSN-ITSVAQL----DGKTLLVNKGTTAEKY---FTKN-HPEIKLLK 143

Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold; Glutamate receptor domain GluR0. These domains are found in the GluR0 proteins that have been shown to function as prokaryotic L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. The GluR0 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 1482688857  37 TLTIVYYEQPGLIYKDNGQMKGVCVDILSDFAKfiQEKY-SKTVTVNyageerEFSGFLKVVQSTPNILGVTNTSITEER 115
Cdd:cd00997     4 TLTVATVPRPPFVFYNDGELTGFSIDLWRAIAE--RLGWeTEYVRVD------SVSALLAAVAEGEADIAIAAISITAER 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1482688857 116 KKILKFTPPFMTTQLVLLTNqNSPALTNLKDLPkvyaGFSALVITGSTHMKYAD 169
Cdd:cd00997    76 EAEFDFSQPIFESGLQILVP-NTPLINSVNDLY----GKRVATVAGSTAADYLR 124

Substrate binding domain of an ABC aspartate/glutamate transporter; the type 2 periplasmic-binding protein fold; This group includes periplasmic aspartate/glutamate binding domain Peb1a and its closely related protein. The Peb1a is an important virulence factor in the food-borne human pathogen Campylobacter jejuni, which has a major role in adherence and host colonization. The Peb1a domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins 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. 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 receptor 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 1482688857  31 KAAGKGTLTI-VYYEQPGLIYKD--NGQMKGVCVDILSDFAKFIQEKYSKTVTVNYAGEEREF-SGFLKVVQSTpnilgv 106
Cdd:cd13691     3 KIKKRGVLRVgVKNDVPGFGYQDpeTGKYEGMEVDLARKLAKKGDGVKVEFTPVTAKTRGPLLdNGDVDAVIAT------ 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857 107 tnTSITEERKKILKFTPPFMTTQLVLLTNQnSPALTNLKDLPKVYAGFSALVITGSTHMKYADMLK-----KQY--YPDL 179
Cdd:cd13691    77 --FTITPERKKSYDFSTPYYTDAIGVLVEK-SSGIKSLADLKGKTVGVASGATTKKALEAAAKKIGigvsfVEYadYPEI 153

                  ..
gi 1482688857 180 NI 181
Cdd:cd13691   154 KT 155

The ligand-binding domain of the kainate subtype KA2 of ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily; This group contains the ligand-binding domain of the KA2 subunit of kainate receptor. While this ligand-binding domain is structurally homologous to the periplasmic binding fold type II superfamily, the N_terminal domain of kainate receptors belongs to the periplasmic-binding fold type I. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated by kainate and glutamate when expressed in heterologous systems. Kainate receptors are involved in excitatory neurotransmission by activating postsynaptic receptors and in inhibitory neurotransmission by modulating release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. Kainate receptors are closely related to AMAP receptors. In contrast of AMPA receptors, kainate receptors play only a minor role in signaling at synapses and their function is not well defined.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857  35 KGTLTIVYYEQPGLIYKDN-------GQMKGVCVDILSDFAKFIQEKYSKTVTVN--YAGEER--EFSGFLKVVQSTPNI 103
Cdd:cd13725     2 KTLVVTTILENPYVMRRPNfqalsgnERFEGFCVDMLRELAELLRFRYRLRLVEDglYGAPEPngSWTGMVGELINRKAD 81

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1482688857 104 LGVTNTSITEERKKILKFTPPFMTTQLVLLTNQNSP 139
Cdd:cd13725    82 LAVAAFTITAEREKVIDFSKPFMTLGISILYRVHMP 117

Amino acid-binding domain of the type 2 periplasmic binding fold superfamily; This subfamily includes the periplasmic binding protein type II (BPBII). This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating. The PBPII proteins share the same architecture as periplasmic binding proteins type I (PBPI), 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 majority of PBPII proteins function in the uptake of small soluble substrates in eubacteria and archaea. 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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1482688857 110 SITEERKKILKFTPPFMTTQLVLLTNQNSPA-LTNLKDLPKvyAGFSALVITGSTHMKYAdmlkKQYYPDLNI 181
Cdd:cd13629    68 TITPERNLKVNFSNPYLVSGQTLLVNKKSAAgIKSLEDLNK--PGVTIAVKLGTTGDQAA----RKLFPKATI 134

Ligated ion channel L-glutamate- and glycine-binding site; This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine. It is found in association with Lig_chan, pfam00060.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857  51 KDNGQMKGVCVDILSDFAKFIQEKYskTVTV-------NYAGEEREFSGFLKVVQSTPNILGVTNTSITEERKKILKFTP 123
Cdd:pfam10613  21 EGNDRYEGFCIDLLKELAEILGFKY--EIRLvpdgkygSLDPTTGEWNGMIGELIDGKADLAVAPLTITSEREKVVDFTK 98

                  ....*
gi 1482688857 124 PFMTT 128
Cdd:pfam10613  99 PFMTL 103

Substrate binding domain of an ABC transporter YxeMNO; the type 2 periplasmic binding protein fold; This group contains cystine-binding domain (YxeM) of a periplasmic receptor-dependent ATP-binding cassette transporter and its closely related proteins. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Likewise, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins 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. 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 receptor 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 1482688857  48 LIYKDNGQMKGVCVDILSDFAKFIQEKYSKTVTvnyageerEFSGFLKVVQSTpNILGVTNT-SITEERKKILKFTPPFM 126
Cdd:cd13709    14 FTFKENGKLKGFEVDVWNAIGKRTGYKVEFVTA--------DFSGLFGMLDSG-KVDTIANQiTITPERQEKYDFSEPYV 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857 127 TTQLVLLTNQNSPALTNLKDLpkvyAGFSALVITGSTHMKYAdmlkKQYYPDLNI---TYapSSETVIKSLTANPKIFS- 202
Cdd:cd13709    85 YDGAQIVVKKDNNSIKSLEDL----KGKTVAVNLGSNYEKIL----KAVDKDNKItikTY--DDDEGALQDVALGRVDAy 154

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1482688857 203 ILDFTEYVGVVRKK-LPIKRQDVDLgNAEELGFIMAKQSDWDGLWKEF--LTDDYRKGVRYKKI 263
Cdd:cd13709   155 VNDRVSLLAKIKKRgLPLKLAGEPL-VEEEIAFPFVKNEKGKKLLEKVnkALEEMRKDGTLKKI 217

Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 periplasmic binding protein fold; This group includes the periplasmic substrate-binding protein ArtJ of the ATP-binding cassette (ABC) transport system from the thermophilic bacterium Geobacillus stearothermophilus, which is specific for arginine, lysine, and histidine. ArtJ 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 two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1482688857 110 SITEERKKILKFTPPFMTTQLVLLTNQNSPALTNLKDL 147
Cdd:cd13624    68 TITEERKKSVDFSDPYYEAGQAIVVRKDSTIIKSLDDL 105

GluR6 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily; This group contains glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR 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 1482688857  44 EQPGLIYKD-------NGQMKGVCVDILSDFAKFIQEKYSKTVTVN--YAGEE---REFSGFLKVVQSTPNILGVTNTSI 111
Cdd:cd13721    11 EEPYVLFKKsdkplygNDRFEGYCIDLLRELSTILGFTYEIRLVEDgkYGAQDdvnGQWNGMVRELIDHKADLAVAPLAI 90

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1482688857 112 TEERKKILKFTPPFMTTQLVLLTNQNSPaLTNLKDLPK 149
Cdd:cd13721    91 TYVREKVIDFSKPFMTLGISILYRKGTP-IDSADDLAK 127

The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) subtype GluR3 of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily; This group contains the ligand-binding domain of the AMPA receptor subunit GluR3, a member of non-NMDA (N-methyl-D-aspartate) type iGluRs which are ligand-gated ion channels that mediate excitatory synaptic transmission in the central nervous system. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of AMPA receptors belongs to the periplasmic-binding fold type I. The AMPA receptors are the most commonly found receptor in the nervous system and sensitive to the artificial glutamate analog, AMPA. They consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1482688857  44 EQPGLIYKDNG-------QMKGVCVDILSDFAKFIQEKYSKTVTVN--YAG---EEREFSGFLKVVQSTPNILGVTNTSI 111
Cdd:cd13728    11 ESPYVMYKKNHeqlegneRYEGYCVDLAYEIAKHVRIKYKLSIVGDgkYGArdpETKIWNGMVGELVYGRADIAVAPLTI 90

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1482688857 112 TEERKKILKFTPPFMTTQLVLLTNQNSPaLTNLKDLPK 149
Cdd:cd13728    91 TLVREEVIDFSKPFMSLGISIMIKKPQP-IESAEDLAK 127