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Conserved domains on  [gi|112490450|pdb|2DE2|A]
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Chain A, DIBENZOTHIOPHENE DESULFURIZATION ENZYME B

Protein Classification

PBP2_DszB domain-containing protein( domain architecture ID 10194323)

PBP2_DszB domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_DszB cd13554
Substrate binding domain of 2'-hydroxybiphenyl-2-sulfinate desulfinase, a member of the type 2 ...
 20-309 6.11e-94

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.


:

Pssm-ID: 270272 [Multi-domain]  Cd Length: 246  Bit Score: 280.55  E-value: 6.11e-94
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       20 DTLTYSNCPVPNALLTASESGFLDAAGIELDVLSGQ-QGTVHFTYDQ--PAYTRFGGEIPPLLSEGLRAPGRTRLLGITP 96
Cdd:cd13554   1 TTLRYSNCPVPNALLTAEESGYLDAAGIDLEVVAGTpTGTVDFTYDQgiPADVVFSGAIPPLLAEGLRAPGRTRLIGITP 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       97 L-LGRQGFFVRDDSPITAAADLAGRRIGVSASAIRilrgqlgdyleldpwrqtlvalGSWEARALLHTLEHGELgvdDVE 175
Cdd:cd13554  81 LdLGRQGLFVRADSPITSAADLEGKRIGMSAGAIR----------------------GSWLARALLHNLEIGGL---DVE 135

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      176 LVPISSPGvdvpaeqleesatvkgadlfpdvaRGQAAVLASGDVDALYSWLPWAGELQA-TGARPVVDLGLDERNAYASV 254
Cdd:cd13554 136 IVPIDSPG------------------------RGQAAALDSGDIDALASWLPWATTLQAtGGARPLVDLGLVEGNSYYST 191

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*
2DE2_A      255 WTVSSGLVRQRPGLVQRLVDAAVDAGLWARDHSDAVTSLHAANLGVSTGAVGQGF 309
Cdd:cd13554 192 WTVRSDFIEQNPEAVKALVEALVRAGDWIQAHPEAVVIIHAAEIGVSPGAVGRTI 246
 
Name Accession Description Interval E-value
PBP2_DszB cd13554
Substrate binding domain of 2'-hydroxybiphenyl-2-sulfinate desulfinase, a member of the type 2 ...
 20-309 6.11e-94

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.


Pssm-ID: 270272 [Multi-domain]  Cd Length: 246  Bit Score: 280.55  E-value: 6.11e-94
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       20 DTLTYSNCPVPNALLTASESGFLDAAGIELDVLSGQ-QGTVHFTYDQ--PAYTRFGGEIPPLLSEGLRAPGRTRLLGITP 96
Cdd:cd13554   1 TTLRYSNCPVPNALLTAEESGYLDAAGIDLEVVAGTpTGTVDFTYDQgiPADVVFSGAIPPLLAEGLRAPGRTRLIGITP 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       97 L-LGRQGFFVRDDSPITAAADLAGRRIGVSASAIRilrgqlgdyleldpwrqtlvalGSWEARALLHTLEHGELgvdDVE 175
Cdd:cd13554  81 LdLGRQGLFVRADSPITSAADLEGKRIGMSAGAIR----------------------GSWLARALLHNLEIGGL---DVE 135

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      176 LVPISSPGvdvpaeqleesatvkgadlfpdvaRGQAAVLASGDVDALYSWLPWAGELQA-TGARPVVDLGLDERNAYASV 254
Cdd:cd13554 136 IVPIDSPG------------------------RGQAAALDSGDIDALASWLPWATTLQAtGGARPLVDLGLVEGNSYYST 191

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*
2DE2_A      255 WTVSSGLVRQRPGLVQRLVDAAVDAGLWARDHSDAVTSLHAANLGVSTGAVGQGF 309
Cdd:cd13554 192 WTVRSDFIEQNPEAVKALVEALVRAGDWIQAHPEAVVIIHAAEIGVSPGAVGRTI 246
TauA COG0715
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ...
 32-346 1.79e-25

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


Pssm-ID: 440479 [Multi-domain]  Cd Length: 297  Bit Score: 104.32  E-value: 1.79e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       32 ALLTASESGFLDAAGIELDVLSGQQGT-------------VHFTYDQPAYTRFGGeippllseglrAPgrTRLLGITPLL 98
Cdd:COG0715  36 PLYVAKEKGYFKKEGLDVELVEFAGGAaalealaagqadfGVAGAPPALAARAKG-----------AP--VKAVAALSQS 102

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       99 GRQGFFVRDDSPITAAADLAGRRIGVSAsairilrgqlgdyleldpwrqtlvalGSWEARALLHTLEHGELGVDDVELVP 178
Cdd:COG0715 103 GGNALVVRKDSGIKSLADLKGKKVAVPG--------------------------GSTSHYLLRALLAKAGLDPKDVEIVN 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      179 ISspgvdvpaeqleesatvkgadlFPDvargQAAVLASGDVDALYSWLPWAGELQATG-ARPVVDLGLDERNAYASVWTV 257
Cdd:COG0715 157 LP----------------------PPD----AVAALLAGQVDAAVVWEPFESQAEKKGgGRVLADSADLVPGYPGDVLVA 210

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      258 SSGLVRQRPGLVQRLVDAAVDAGLWARDHSDAVTSLHAANLGVSTGAVGQGFGADFqqRLVPRLDHDALALLERTQQFLL 337
Cdd:COG0715 211 SEDFLEENPEAVKAFLRALLKAWAWAAANPDEAAAILAKATGLDPEVLAAALEGDL--RLDPPLGAPDPARLQRVADFLV 288


                ....*....
2DE2_A      338 TNNLLQEPV 346
Cdd:COG0715 289 ELGLLPKDV 297
NMT1 pfam09084
NMT1/THI5 like; This family contains the NMT1 and THI5 proteins. These proteins are proposed ...
 33-289 4.63e-08

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.


Pssm-ID: 430398 [Multi-domain]  Cd Length: 216  Bit Score: 52.99  E-value: 4.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A         33 LLTASESGFLDAAGIELDVLSGQQ----------GTVHFT-YDQPAYTRFGGEIPPLLSEGlrapgrtRLLGITPllgrQ 101
Cdd:pfam09084   7 LYVAQEKGYFKEEGLDVEIVEPADpsdatqlvasGKADFGvSYQESVLLARAKGLPVVSVA-------ALIQHPL----S 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A        102 GFFVRDDSPITAAADLAGRRIGVSasairilrgqlgdyleldpwrqtlvalGSWEARALLHT-LEHGELGVDDVELVPis 180
Cdd:pfam09084  76 GVISLKDSGIKSPKDLKGKRIGYS---------------------------GSPFEEALLKAlLKKDGGDPDDVTIVN-- 126

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A        181 spgvdvpaeqleesatVKGADLFPDVARGQAAVLASGdvdaLYSWLPwaGELQATGARPVVDL--GLDERNAYASVWTVS 258
Cdd:pfam09084 127 ----------------VGGMNLFPALLTGKVDAAIGG----YYNWEG--VELKLEGVELNIFAlaDYGVPDYYSLVLITN 184

                         250       260       270
                  ....*....|....*....|....*....|.
2DE2_A        259 SGLVRQRPGLVQRLVDAAVDAGLWARDHSDA 289
Cdd:pfam09084 185 EAFLKENPELVRAFLRATLRGYQYALAHPEE 215
SsuA_fam TIGR01728
ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this ...
 32-358 1.23e-07

ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins. [Transport and binding proteins, Other]


Pssm-ID: 130789 [Multi-domain]  Cd Length: 288  Bit Score: 52.36  E-value: 1.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A         32 ALLTASESGFLDAAGIELDVlsgqqGTVHFTYDQPAYTRFG---------GEIPPLLSEGLRAPgrTRLLGITPLLGRQG 102
Cdd:TIGR01728  12 ALALAKEKGLLEKELGKTKV-----EWVEFPAGPPALEALGagsldfgyiGPGPALFAYAAGAD--IKAVGLVSDNKATA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A        103 FFVRDDSPITAAADLAGRRIGVsasairiLRGQLGDYLELdpwrqtlvalgsweaRALLHTLehgeLGVDDVELVPISSP 182
Cdd:TIGR01728  85 IVVIKGSPIRTVADLKGKRIAV-------PKGGSGHDLLL---------------RALLKAG----LSGDDVTILYLGPS 138

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A        183 GVdvpaeqleesatvkgadlfpdvargqAAVLASGDVDALYSWLPWAGELQA-TGARPVVDLGLDERNAYASVWTVSSGL 261
Cdd:TIGR01728 139 DA--------------------------RAAFAAGQVDAWAIWEPWGSALVEeGGARVLANGEGIGLPGQPGFLVVRREF 192

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A        262 VRQRPGLVQRLVDAAVDAGLWARDHSDAVTSLHAANLGVSTGAVGQGFGADFQQRLVPRLDHDALALLErTQQFLLTNNL 341
Cdd:TIGR01728 193 AEAHPEQVQRVLKVLVKARKWAEENPEESAKILAKELGLSQAVVEETVLNRRFLRVEVISDAVVDALQA-MADFFYAAGL 271

                         330
                  ....*....|....*..
2DE2_A        342 LQEPVALDQWAAPEFLN 358
Cdd:TIGR01728 272 LKKKPDLKDAVDRSFLK 288
 
Name Accession Description Interval E-value
PBP2_DszB cd13554
Substrate binding domain of 2'-hydroxybiphenyl-2-sulfinate desulfinase, a member of the type 2 ...
 20-309 6.11e-94

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.


Pssm-ID: 270272 [Multi-domain]  Cd Length: 246  Bit Score: 280.55  E-value: 6.11e-94
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       20 DTLTYSNCPVPNALLTASESGFLDAAGIELDVLSGQ-QGTVHFTYDQ--PAYTRFGGEIPPLLSEGLRAPGRTRLLGITP 96
Cdd:cd13554   1 TTLRYSNCPVPNALLTAEESGYLDAAGIDLEVVAGTpTGTVDFTYDQgiPADVVFSGAIPPLLAEGLRAPGRTRLIGITP 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       97 L-LGRQGFFVRDDSPITAAADLAGRRIGVSASAIRilrgqlgdyleldpwrqtlvalGSWEARALLHTLEHGELgvdDVE 175
Cdd:cd13554  81 LdLGRQGLFVRADSPITSAADLEGKRIGMSAGAIR----------------------GSWLARALLHNLEIGGL---DVE 135

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      176 LVPISSPGvdvpaeqleesatvkgadlfpdvaRGQAAVLASGDVDALYSWLPWAGELQA-TGARPVVDLGLDERNAYASV 254
Cdd:cd13554 136 IVPIDSPG------------------------RGQAAALDSGDIDALASWLPWATTLQAtGGARPLVDLGLVEGNSYYST 191

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*
2DE2_A      255 WTVSSGLVRQRPGLVQRLVDAAVDAGLWARDHSDAVTSLHAANLGVSTGAVGQGF 309
Cdd:cd13554 192 WTVRSDFIEQNPEAVKALVEALVRAGDWIQAHPEAVVIIHAAEIGVSPGAVGRTI 246
PBP2_NrtA_SsuA_CpmA_like cd01008
Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of ...
 21-279 4.62e-29

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.


Pssm-ID: 270229 [Multi-domain]  Cd Length: 212  Bit Score: 111.61  E-value: 4.62e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       21 TLTYSNCPVPNALLTASESGFLD--AAGIELDVLSGQQG-TVHFTYDQ-PAYTRFGGEIPPLLSEGlrAPGRTRLLGITP 96
Cdd:cd01008   3 RIGYQAGPLAGPLIVAKEKGLFEkeKEGIDVEWVEFTSGpPALEALAAgSLDFGTGGDTPALLAAA--GGVPVVLIAALS 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       97 LLGR-QGFFVRDDSPITAAADLAGRRIGVSAsairilrgqlgdyleldpwrqtlvalGSWEARALLHTLEHGELGVDDVE 175
Cdd:cd01008  81 RSPNgNGIVVRKDSGITSLADLKGKKIAVTK--------------------------GTTGHFLLLKALAKAGLSVDDVE 134

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      176 LVPISSPGvdvpaeqleesatvkgadlfpdvargQAAVLASGDVDALYSWLPWAGELQATG-ARPVVDLGLDErNAYASV 254
Cdd:cd01008 135 LVNLGPAD--------------------------AAAALASGDVDAWVTWEPFLSLAEKGGdARIIVDGGGLP-YTDPSV 187

                       250       260
                ....*....|....*....|....*
2DE2_A      255 WTVSSGLVRQRPGLVQRLVDAAVDA 279
Cdd:cd01008 188 LVARRDFVEENPEAVKALLKALVEA 212
TauA COG0715
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ...
 32-346 1.79e-25

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


Pssm-ID: 440479 [Multi-domain]  Cd Length: 297  Bit Score: 104.32  E-value: 1.79e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       32 ALLTASESGFLDAAGIELDVLSGQQGT-------------VHFTYDQPAYTRFGGeippllseglrAPgrTRLLGITPLL 98
Cdd:COG0715  36 PLYVAKEKGYFKKEGLDVELVEFAGGAaalealaagqadfGVAGAPPALAARAKG-----------AP--VKAVAALSQS 102

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       99 GRQGFFVRDDSPITAAADLAGRRIGVSAsairilrgqlgdyleldpwrqtlvalGSWEARALLHTLEHGELGVDDVELVP 178
Cdd:COG0715 103 GGNALVVRKDSGIKSLADLKGKKVAVPG--------------------------GSTSHYLLRALLAKAGLDPKDVEIVN 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      179 ISspgvdvpaeqleesatvkgadlFPDvargQAAVLASGDVDALYSWLPWAGELQATG-ARPVVDLGLDERNAYASVWTV 257
Cdd:COG0715 157 LP----------------------PPD----AVAALLAGQVDAAVVWEPFESQAEKKGgGRVLADSADLVPGYPGDVLVA 210

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      258 SSGLVRQRPGLVQRLVDAAVDAGLWARDHSDAVTSLHAANLGVSTGAVGQGFGADFqqRLVPRLDHDALALLERTQQFLL 337
Cdd:COG0715 211 SEDFLEENPEAVKAFLRALLKAWAWAAANPDEAAAILAKATGLDPEVLAAALEGDL--RLDPPLGAPDPARLQRVADFLV 288


                ....*....
2DE2_A      338 TNNLLQEPV 346
Cdd:COG0715 289 ELGLLPKDV 297
PBP2_ThiY_THI5_like_1 cd13652
Putative substrate binding domain of an ABC-type transporter similar to ThiY/THI5; the type 2 ...
 89-279 9.84e-11

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.


Pssm-ID: 270370 [Multi-domain]  Cd Length: 217  Bit Score: 60.86  E-value: 9.84e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       89 TRLLGITPLLGRQGFFVRDDSPITAAADLAGRRIGVSASairilrGQLGDYleldpwrqtlvalgswearALLHTLEHGE 168
Cdd:cd13652  78 AEGLGTTPGYGPFAIVVRADSGITSPADLVGKKIAVSTL------TNILEY-------------------TTNAYLKKNG 132

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      169 LGVDDVELVPISspgvdvpaeqleesatvkgadlFPDvaRGQAavLASGDVDALYSWLPWAGELQATGARPVVDLGLDER 248
Cdd:cd13652 133 LDPDKVEFVEVA----------------------FPQ--MVPA--LENGNVDAAVLAEPFLSRARSSGAKVVASDYADPD 186

                       170       180       190
                ....*....|....*....|....*....|.
2DE2_A      249 NAYASVWTVSSGLVRQRPGLVQRLVDAAVDA 279
Cdd:cd13652 187 PHSQATMVFSADFARENPEVVKKFLRAYLEA 217
PBP2_SsuA cd13557
Substrate binding domain of sulfonate binding protein, a member of the type 2 periplasmic ...
 101-300 1.08e-10

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.


Pssm-ID: 270275  Cd Length: 275  Bit Score: 61.54  E-value: 1.08e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      101 QGFFVRDDSPITAAADLAGRRIGVSasairilRGQLGDYLeldpwrqtlvalgswearaLLHTLEHGELGVDDVELVPIS 180
Cdd:cd13557  85 EAILVPKDSPIKTVADLKGKKIAFQ-------KGSSAHYL-------------------LVKALEKAGLTLDDIEPVYLS 138

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      181 spgvdvPAEqleesatvkgadlfpdvarGQAAvLASGDVDALYSWLPW-AGELQATGARPVVDL-GLDERNAYasvWTVS 258
Cdd:cd13557 139 ------PAD-------------------ARAA-FEQGQVDAWAIWDPYlAAAELTGGARVLADGeGLVNNRSF---YLAA 189

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
2DE2_A      259 SGLVRQRPGLVQRLVDAAVDAGLWARDHSDAVTSLHAANLGV 300
Cdd:cd13557 190 RDFAKDNPEAIQIVLEELNKAGEWANTNRDEAAKLLAESLGI 231
PBP2_SsuA_like_2 cd13558
Putative substrate binding domain of sulfonate binding protein, the type 2 periplasmic binding ...
 71-327 1.89e-08

Putative substrate binding domain of sulfonate binding 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.


Pssm-ID: 270276  Cd Length: 267  Bit Score: 54.60  E-value: 1.89e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       71 FGGEIPPLLSegLRAPGRTRLLGI--TPLLGrQGFFVRDDSPITAAADLAGRRIGVSasairilRGQLGDYLeldpwrqt 148
Cdd:cd13558  52 GAGDTPPLFA--AAAGAPIKIVAAlrGDVNG-QALLVPKDSPIRSVADLKGKRVAYV-------RGSISHYL-------- 113

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      149 lvalgswearaLLHTLEHGELGVDDVELVPISspgvdvPAEqleesatvkgadlfpdvarGQAAvLASGDVDALYSWLPW 228
Cdd:cd13558 114 -----------LLKALEKAGLSPSDVELVFLT------PAD-------------------ALAA-FASGQVDAWATWGPY 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      229 AGELQATGARPVVDLGLDERNAYaSVWTVSSG--LVRQRPGLVQRLVDAAVDAGLWARDHSDAVTSLHAANLGVSTGAVG 306
Cdd:cd13558 157 VARAERRGGARVLVTGEGLILGL-SFVVAARPalLDPAKRAAIADFLARLARAQAWANAHPDEWAKAYAAETGLPPEVAA 235

                       250       260
                ....*....|....*....|.
2DE2_A      307 QGFGAdfQQRLVPRLDHDALA 327
Cdd:cd13558 236 AIFAR--RSAPVVPIDAQVIA 254
NMT1 pfam09084
NMT1/THI5 like; This family contains the NMT1 and THI5 proteins. These proteins are proposed ...
 33-289 4.63e-08

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.


Pssm-ID: 430398 [Multi-domain]  Cd Length: 216  Bit Score: 52.99  E-value: 4.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A         33 LLTASESGFLDAAGIELDVLSGQQ----------GTVHFT-YDQPAYTRFGGEIPPLLSEGlrapgrtRLLGITPllgrQ 101
Cdd:pfam09084   7 LYVAQEKGYFKEEGLDVEIVEPADpsdatqlvasGKADFGvSYQESVLLARAKGLPVVSVA-------ALIQHPL----S 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A        102 GFFVRDDSPITAAADLAGRRIGVSasairilrgqlgdyleldpwrqtlvalGSWEARALLHT-LEHGELGVDDVELVPis 180
Cdd:pfam09084  76 GVISLKDSGIKSPKDLKGKRIGYS---------------------------GSPFEEALLKAlLKKDGGDPDDVTIVN-- 126

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A        181 spgvdvpaeqleesatVKGADLFPDVARGQAAVLASGdvdaLYSWLPwaGELQATGARPVVDL--GLDERNAYASVWTVS 258
Cdd:pfam09084 127 ----------------VGGMNLFPALLTGKVDAAIGG----YYNWEG--VELKLEGVELNIFAlaDYGVPDYYSLVLITN 184

                         250       260       270
                  ....*....|....*....|....*....|.
2DE2_A        259 SGLVRQRPGLVQRLVDAAVDAGLWARDHSDA 289
Cdd:pfam09084 185 EAFLKENPELVRAFLRATLRGYQYALAHPEE 215
SsuA_fam TIGR01728
ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this ...
 32-358 1.23e-07

ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins. [Transport and binding proteins, Other]


Pssm-ID: 130789 [Multi-domain]  Cd Length: 288  Bit Score: 52.36  E-value: 1.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A         32 ALLTASESGFLDAAGIELDVlsgqqGTVHFTYDQPAYTRFG---------GEIPPLLSEGLRAPgrTRLLGITPLLGRQG 102
Cdd:TIGR01728  12 ALALAKEKGLLEKELGKTKV-----EWVEFPAGPPALEALGagsldfgyiGPGPALFAYAAGAD--IKAVGLVSDNKATA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A        103 FFVRDDSPITAAADLAGRRIGVsasairiLRGQLGDYLELdpwrqtlvalgsweaRALLHTLehgeLGVDDVELVPISSP 182
Cdd:TIGR01728  85 IVVIKGSPIRTVADLKGKRIAV-------PKGGSGHDLLL---------------RALLKAG----LSGDDVTILYLGPS 138

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A        183 GVdvpaeqleesatvkgadlfpdvargqAAVLASGDVDALYSWLPWAGELQA-TGARPVVDLGLDERNAYASVWTVSSGL 261
Cdd:TIGR01728 139 DA--------------------------RAAFAAGQVDAWAIWEPWGSALVEeGGARVLANGEGIGLPGQPGFLVVRREF 192

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A        262 VRQRPGLVQRLVDAAVDAGLWARDHSDAVTSLHAANLGVSTGAVGQGFGADFQQRLVPRLDHDALALLErTQQFLLTNNL 341
Cdd:TIGR01728 193 AEAHPEQVQRVLKVLVKARKWAEENPEESAKILAKELGLSQAVVEETVLNRRFLRVEVISDAVVDALQA-MADFFYAAGL 271

                         330
                  ....*....|....*..
2DE2_A        342 LQEPVALDQWAAPEFLN 358
Cdd:TIGR01728 272 LKKKPDLKDAVDRSFLK 288
Periplasmic_Binding_Protein_Type_2 cd00648
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 21-259 1.79e-07

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.


Pssm-ID: 270214 [Multi-domain]  Cd Length: 196  Bit Score: 51.03  E-value: 1.79e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       21 TLTYSNCPVP---NALLTASESGFlDAAGIELDVLSG-QQGTVHFTY-DQPAYTRFGGEIPPLL-SEGLRAPGRTRLLGI 94
Cdd:cd00648   1 TLTVASIGPPpyaGFAEDAAKQLA-KETGIKVELVPGsSIGTLIEALaAGDADVAVGPIAPALEaAADKLAPGGLYIVPE 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       95 TPLlGRQGFFVRDDSPI---TAAADLAGRRIGVSASairilrgqlgdyleldpwrqtlvalGSWEARALLHTLEHGELGV 171
Cdd:cd00648  80 LYV-GGYVLVVRKGSSIkglLAVADLDGKRVGVGDP-------------------------GSTAVRQARLALGAYGLKK 133

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      172 DDVELVPISSPgvdvpaeqleesatvkgadlfpdvaRGQAAVLASGDVDALYSWLPWAGELQAtGARPVVDLGLDER-NA 250
Cdd:cd00648 134 KDPEVVPVPGT-------------------------SGALAAVANGAVDAAIVWVPAAERAQL-GNVQLEVLPDDLGpLV 187


                ....*....
2DE2_A      251 YASVWTVSS 259
Cdd:cd00648 188 TTFGVAVRK 196
PBP2_SsuA_like_1 cd13556
Substrate binding domain of putative sulfonate binding protein, a member of the type 2 ...
 105-301 2.39e-07

Substrate binding domain of putative sulfonate binding protein, a member of the type 2 periplasmic binding fold superfamily; 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.


Pssm-ID: 270274  Cd Length: 265  Bit Score: 51.32  E-value: 2.39e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      105 VRDDSPITAAADLAGRRIGVSasairilRGQlgdylelDPWRQTLVALgswearallhtLEHGeLGVDDVELVPISSPgv 184
Cdd:cd13556  89 VRKDSPIRSVADLKGKKVAVT-------KGT-------DPYIFLLRAL-----------NTAG-LSKNDIEIVNLQHA-- 140

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      185 dvpaeqleesatvkgadlfpdvaRGQAAvLASGDVDAlyswlpWAGeLQATGARPVVDLG--LDERNAYASVW---TVSS 259
Cdd:cd13556 141 -----------------------DGRTA-LEKGDVDA------WAG-LDPFMAQTELENGsrLFYRNPDFNTYgvlNVRE 189

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
2DE2_A      260 GLVRQRPGLVQRLVDAAVDAGLWARDHSDAVTSLHAANLGVS 301
Cdd:cd13556 190 DFAKRHPDAVRRVLKVYEKARKWAITHPDELAQILASESKLS 231
TauA COG4521
ABC-type taurine transport system, periplasmic component [Inorganic ion transport and ...
 105-289 2.74e-06

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


Pssm-ID: 443595 [Multi-domain]  Cd Length: 332  Bit Score: 48.71  E-value: 2.74e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      105 VRDDSPITAAADLAGRRIGVSasairilrgqlgdyleldpwrqtlvaLGSWEARALLHTLEHGELGVDDVELVpisspgv 184
Cdd:COG4521 115 VRNGSGITSPKDLKGKKIAVP--------------------------FGSTSHYSLLAALKHAGIDPSDVTIL------- 161

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      185 dvpaeqleesatvkgaDLFPDVArgqAAVLASGDVDALYSWLPWAGELQATG-----ARPVVDLGLdernAYASVWTVSS 259
Cdd:COG4521 162 ----------------NMQPPEI---AAAWQRGDIDAAYVWDPALSELKKSGkvlitSAELAKWGA----PTFDVWVVRK 218

                       170       180       190
                ....*....|....*....|....*....|
2DE2_A      260 GLVRQRPGLVQRLVDAAVDAGLWARDHSDA 289
Cdd:COG4521 219 DFAEENPDFVAAFLKVLADAVADYRADPAA 248
PBP2_sulfate_ester_like cd13555
Sulfate ester binding protein-like, the type 2 periplasmic binding protein fold; This ...
 71-285 7.33e-06

Sulfate ester 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.


Pssm-ID: 270273  Cd Length: 268  Bit Score: 46.95  E-value: 7.33e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A       71 FGGEIPPLLsegLRAPG-RTRLLGITPLLGRQGFFVRDDSPITAAADLAGRRIGVSasairilRGQlgdyleldPWRQTL 149
Cdd:cd13555  66 VYGDLPAII---GRAAGlDTKLLLSSGSGNNAYLVVPPDSTIKSVKDLKGKKVAVQ-------KGT--------AWQLTF 127

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      150 valgsweARALLhtlEHGeLGVDDVELVpisspgvdvpaeqleesatvkgaDLFPDVArgqAAVLASGDVDALYSWLPWa 229
Cdd:cd13555 128 -------LRILA---KNG-LSEKDFKIV-----------------------NLDAQDA---QAALASGDVDAAFTGYEA- 169

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*....
2DE2_A      230 GELQATGARPVVDLGLDERNAY---ASVWtVSSGLVRQRPGLVQRLVDAAVDAGLWARD 285
Cdd:cd13555 170 LKLEDQGAGKIIWSTKDKPEDWttqSGVW-ARTDFIKENPDVVQRIVTALVKAARWVSQ 227
PBP2_SsuA_like_6 cd13563
Putative substrate binding domain of sulfonate binding protein-like, a member of the type 2 ...
 111-279 1.03e-03

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.


Pssm-ID: 270281 [Multi-domain]  Cd Length: 208  Bit Score: 39.91  E-value: 1.03e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      111 ITAAADLAGRRIGVSASAIrilrgqlGDYLeldpwrqtlvalgswearaLLHTLEHGELGVDDVELVPISspgvdvpaeq 190
Cdd:cd13563  92 IKSIADLKGKTVAVEEGSV-------SHFL-------------------LLNALEKAGLTEKDVKIVNMT---------- 135

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2DE2_A      191 leesatvkgadlfPDVArgqAAVLASGDVDALYSWLPWAGE-LQATGARPVVDlGLDERNAYASVWTVSSGLVRQRPGLV 269
Cdd:cd13563 136 -------------AGDA---GAAFIAGQVDAAVTWEPWLSNaLKRGKGKVLVS-SADTPGLIPDVLVVREDFIKKNPEAV 198

                       170
                ....*....|
2DE2_A      270 QRLVDAAVDA 279
Cdd:cd13563 199 KAVVKAWFDA 208
PBP2_Cystine_like_1 cd13713
Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 ...
 99-126 1.72e-03

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.


Pssm-ID: 270431 [Multi-domain]  Cd Length: 218  Bit Score: 39.19  E-value: 1.72e-03
                        10        20
                ....*....|....*....|....*...
2DE2_A       99 GRQgFFVRDDSPITAAADLAGRRIGVSA 126
Cdd:cd13713  87 GAQ-IFVRKDSTITSLADLKGKKVGVVT 113
PBP2_BztA cd13692
Substrate bindng domain of ABC glutamate/glutamine/aspartate/asparagine transporter; the type ...
 101-126 2.04e-03

Substrate bindng domain of ABC glutamate/glutamine/aspartate/asparagine transporter; the type 2 periplasmic binding protein fold; BztA is the periplamic-binding protein component of ABC transporter specific for carboxylic amino acids, glutamine and asparagine. The BZtA 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.


Pssm-ID: 270410 [Multi-domain]  Cd Length: 236  Bit Score: 39.15  E-value: 2.04e-03
                        10        20
                ....*....|....*....|....*.
2DE2_A      101 QGFFVRDDSPITAAADLAGRRIGVSA 126
Cdd:cd13692 101 QGFLVRKDSGITSAKDLDGATICVQA 126
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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