2G29,3UIF,3IX1,2I48,2DE4,2DE3,2DE2,3QSL,3KSJ


Conserved Protein Domain Family
PBP2_NrtA_SsuA_CpmA_like
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cd01008: PBP2_NrtA_SsuA_CpmA_like 
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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.
Links
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Statistics
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PSSM-Id: 270229
Aligned: 40 rows
Threshold Bit Score: 111.611
Created: 1-Nov-2000
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
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chemical
Conserved site includes 9 residues -Click on image for an interactive view with Cn3D
Feature 1:chemical substrate binding site [chemical binding site]
Evidence:
  • Structure:2G29; the periplasmic nitrate-Binding protein NrtA from Synechocystis sp. binds nitrate ion, contacts 4A.
  • Structure:3IX1; the periplasmic ThiY protein from Bacillus halodurans binds FAMP (N-Formyl-4-Amino-5-Aminomethyl-2-Methylpyrimidine), contacts at 4A.
  • Structure:3KSJ; the alkanesulfonate-binding protein SsuA From Xabthomonas axonopodis binds MES (2-(N-morpholino)ethanesulfonic acid), contacts 4A.
  • Structure:2I48; the bicarbonate transport protein CmpA from Synechocystis sp. in complex with carbonic acid, contacts at 4A.
  • Structure:3QSL; Cae31940 protein from Bordetella bronchiseptica binds citric acid, contacts at 4A.
  • Structure:2DE4; desulfurization enzyme DszB C27s mutant from Rhodococcus sp. in complex With biphenyl-2-sulfinic acid, contacts at 4A.
  • Structure:2DE3; desulfurization enzyme DszB C27s mutant from Rhodococcus sp. in complex With biphenyl-2-sulfinic acid, contacts at 4A.
Scroll to Sequence Alignment Display
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1               #                                     #                                  
2G29_A        34 TAKLGFIAltd--aaPLIIAKEKGFyaky---gmpDVEVLKqa-sWGTTRDNLvlgsasggiDGAHIl-tPMPYLItmgt 106 Synechocystis sp.
3IX1_A         4 TVEVMLDWypnavhtFLYVAIENGYfae----eglDVDIVFpt-nPTDPIQLTasg----aiPLALSy-qPDVILArsk- 72  Bacillus halodu...
2I48_A        37 NIKLGYIPive--aaPLIIAQEKGFfaky---gmtGVEVSKqa-nWASARDNVtigsqgggiDGGQWq-mPMPHLItegi 109 Synechocystis sp.
2DE4_A        21 TLTYSNSPvp----nALLTASESGFlda----agiELDVLSg--qQGTVHFTYdq-----paYTRFGg-eIPPLLSeglr 84  Rhodococcus sp.
2DE3_A        21 TLTYSNSPvp----nALLTASESGFlda----agiELDVLSg--qQGTVHFTYdq-----paYTRFGg-eIPPLLSeglr 84  Rhodococcus sp....
2DE2_A        21 TLTYSNCPvp----nALLTASESGFlda----agiELDVLSg--qQGTVHFTYdq-----paYTRFGg-eIPPLLSeglr 84  Rhodococcus sp....
EDX86506      54 SLTMGSIPwag--qvPMYIAQDKGYyee----eglDFELRLfg-sGSEYIAAFlsd----qlDAVAPv-tSEAVLIksqg 121 Synechococcus s...
YP_001239307  41 TVRLTWGLs-----gLNLIAKERGEfekllakdgiKVEWLGpfpnHAPTLQAVtgg----taDFSFGgstTPALAAiia- 110 Bradyrhizobium ...
YP_706970     42 TLKVFDPGns----gAIAVGKRDGTydealaplgaKIEWVKttpgFSSNLKLFntg----elDIQTGa-ySPVVGAlsk- 111 Rhodococcus sp....
YP_556206     44 TVRVGWGYg-----sLPDIARQRGVfektlaakgiKVEWVGpfpnHAPSIQAVvgg----saDFGFWgstTPALAAmla- 113 Burkholderia xe...

Feature 1                              #                                       #                 
2G29_A       107 vtdgkptPMYILARLnv---ngQGIQLGNnykdlkvgtd-----aaplkeafaKVTDPKVAMTFPg-------------- 164 Synechocystis sp.
3IX1_A        73 -----dlPVVSVASVvrs--plNHVMFLAeqdf----------------dspaDLVGLTVGYPGIp-------------- 115 Bacillus halodu...
2I48_A       110 itngnkvPMYVLAQLit---qgNGIAVAPmhegkgvnlditkaadyikgfnktNGRKFKAAHTFPn-------------- 172 Synechocystis sp.
2DE4_A        85 ----apgRTRLLGITpll--grQGFFVRDdspi----------------taaaDLAGRRIGVSASairilrgqlgdylel 142 Rhodococcus sp.
2DE3_A        85 ----apgRTRLLGITpll--grQGFFVRDdspi----------------taaaDLAGRRIGVSASairilrgqlgdylel 142 Rhodococcus sp....
2DE2_A        85 ----apgRTRLLGITpll--grQGFFVRDdspi----------------taaaDLAGRRIGVSASairilrgqlgdylel 142 Rhodococcus sp....
EDX86506     122 ----kdfKIVMVQDNsv---giDGILARDsit------------------sieDFRGKRVAVETSa-------------- 162 Synechococcus s...
YP_001239307 111 -----gsPLVFTQFVvye-prtTAIIARDdsgi----------------nkveDLVGKSVAVNRSg-------------- 154 Bradyrhizobium ...
YP_706970    112 -----dvGVRIFATSdpynkdqAGIIARPesgi----------------tsvaDLPGKRIAVNPAg-------------- 156 Rhodococcus sp....
YP_556206    114 -----gsPLVFNAFDiys-prsTAIIVKKssgi----------------nsvaDLAGRKVAINRSg-------------- 157 Burkholderia xe...

Feature 1                     #                                                                  
2G29_A       165 -----------gTHDMWIRYWLAAGGmepgkDFSTIVVpp--------------------------aqMVANVKVNaMES 207 Synechocystis sp.
3IX1_A       116 ------------VNEPILKTMVEAAGgd-yeQVHLMDVgf---------------------------eLGASIVSGrADA 155 Bacillus halodu...
2I48_A       173 -----------vNQDFWIRYWFAAGGvdpdtDIDLLAVpp--------------------------aeTVQGMRNGtMDA 215 Synechocystis sp.
2DE4_A       143 dpwrqtlvalgsWEARALLHTLEHGElg-vdDVELVPIsspgvdvpaeqleesatvkgadlfpdvargQAAVLASGdVDA 221 Rhodococcus sp.
2DE3_A       143 dpwrqtlvalgsWEARALLHTLEHGElg-vdDVELVPIsspgvdvpaeqleesatvkgadlfpdvargQAAVLASGdVDA 221 Rhodococcus sp....
2DE2_A       143 dpwrqtlvalgsWEARALLHTLEHGElg-vdDVELVPIsspgvdvpaeqleesatvkgadlfpdvargQAAVLASGdVDA 221 Rhodococcus sp....
EDX86506     163 ------------VGYFFLLQVLKEAGls-kdDITAINTep--------------------------saAAAAFQSGnVDI 203 Synechococcus s...
YP_001239307 155 ------------LGEFLLVAALEKHKvd-rsKVKFVYLnp--------------------------pdAAPALASGkVDA 195 Bradyrhizobium ...
YP_706970    157 ------------KGEYITLKALTQAGip-vdSVERVPLqq--------------------------adAASAFSTGqVDA 197 Rhodococcus sp....
YP_556206    158 ------------LGEFLLIAALEKNHid-rsKVEFVYLnp--------------------------pdAAPAFAQGvVDA 198 Burkholderia xe...

Feature 1          ##    #                           #                          
2G29_A       208 FCVGe--PWPLQTVNQg-vGYQALTTgqlw-kdhpEKAFGMRAdwvdqNPKAAKALLMAVMEA 266 Synechocystis sp.
3IX1_A       156 VVGTyinHEYPVLKHEghdISYFNPVdygv-peydELVLISNEayveeSGEVLAAFWRAALKG 217 Bacillus halodurans C-125
2I48_A       216 FSTGd--PWPYRIVTEn-iGYMAGLTaqiw-pyhpEEYLAIRAdwvdkNPKATKALLKGIMEA 274 Synechocystis sp.
2DE4_A       222 LYSWl--PWAGELQATg--ARPVVDLglde-rnayASVWTVSSglvrqRPGLVQRLVDAAVDA 279 Rhodococcus sp.
2DE3_A       222 LYSWl--PWAGELQATg--ARPVVDLglde-rnayASVWTVSSglvrqRPGLVQRLVDAAVDA 279 Rhodococcus sp. IGTS8
2DE2_A       222 LYSWl--PWAGELQATg--ARPVVDLglde-rnayASVWTVSSglvrqRPGLVQRLVDAAVDA 279 Rhodococcus sp. IGTS8
EDX86506     204 AVTYa--PFLQEAADAtedGRIIYDSsqmp--taiSDLYVFDTafaeeNPQTVQAFVNATLRG 262 Synechococcus sp. PCC 7335
YP_001239307 196 WSMWs--PGVDIARLDy-kAHDIFLEgrdlefqidYTSYLTTRkfaaeNPALVRAVNDAFRAE 255 Bradyrhizobium sp. BTAi1
YP_706970    198 WASFl-iPYQEAKAKGa--VEIATEAsig---svdSTIIAGRTkvleeHPDVVEKFLEVTQQL 254 Rhodococcus sp. RHA1
YP_556206    199 WSMWs--PAVDIARYTn-nAKDIFNEgrdldflidYSSLVTRRkfteeNSELIRAVIDAYYVE 258 Burkholderia xenovorans LB400

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