Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_13

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cd08517: PBP2_NikA_DppA_OppA_like_13 
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.
This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.
Statistics
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PSSM-Id: 173882
View PSSM: cd08517
Aligned: 58 rows
Threshold Bit Score: 506.706
Threshold Setting Gi: 42525914
Created: 27-Nov-2009
Updated: 2-Oct-2020
Structure
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Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
NP_142742    38 GGTLIVLYWGDPksFNPDAqvd-daGYGIAn-qIFCKLVTLDrdyNVIPDLAYKWEISdDGKVYTFYLNPnATWHDGVPV 115 Pyrococcus horik...
NP_971012    39 KTTLIVGAGGDPmsWNPDSlpd-dnGYPIFq-nIFNRLVKLDaskNIIPDLAESWDISpDGKEITFYLHT-AEWHDGKPV 115 Treponema dentic...
ZP_03636508  34 EQVFVFSLAGDPatYHPDLktd-dfAYIINq-nVFNRLVKLGpndNVLPDLAESWEFSnNDKTLTFHLHDgVKWHDGEPF 111 Holdemania filif...
ZP_03635356  46 DQTLIMVTTQDPqsFNPDFksd-dgAWPINq-nIFNRLVKLGnntKINLDLAESYEFSeDGMQLTFHLHDgVKWHDGEPF 123 Holdemania filif...
ZP_03635358  44 GGTYVMRSHGDPnsFNPNMkt--ddLQLPAtynIFNRLVKMTvdnHVVPDLATDWEFSeDGMELTFNLREnVKWHDGEPF 121 Holdemania filif...
ZP_03635359  44 GGTYIIRQATDPgsFNPDVkgddmaTYTATn--VFNRLVKTTastEIIPDLAESWEFSeDGKTLTFHLYEnVKWHDGEPF 121 Holdemania filif...
ZP_03635381  43 GGTYIVRGAGDPysFNPDLkv--ddWGVVTyqnIFNRLVKQTvsnEVVGDLAESWEFSdDGLTLTFHLHEgVKWHDGEPF 120 Holdemania filif...
ZP_03635351  40 QDVLIYAVNGDPqsFNPDMksd-dyAYQINq-nIYNRLVKLNandQILPDLAKSWEFSeDGLTLTFHLQEgVKWHDGEPF 117 Holdemania filif...
ZP_03635353  38 EDTLIVVSSGDPvnFHPDFksd-dnAWGPNq-nIFNRLIKLNaydQVIPDLAETWEWNdDSTQVTFHLHEgVKWHDGEPF 115 Holdemania filif...
ZP_03635354  42 IGTFITAVQGDPssFNPDMksd-dyLWPMAq-nLFNRLYKLApgdVPIPDLATSYEWSdDNMTLTFHLRDgVKWHDGEPL 119 Holdemania filif...
NP_142742   116 TAEDVKWTFEAIKKykgiaygiihadniekIEVVDNYTVRFYLkepfaPFLSFLawygtFILPKHIYEkysdwldpkNPY 195 Pyrococcus horik...
NP_971012   116 TADDVKYTFDYIAKkntyllys-rlqiideIVVKDSKTVVFKLkvpdvSLVANLgwyasFVLPKHIFDngqe-wednIAA 193 Treponema dentic...
ZP_03636508 112 TSADVKWTYDTLMAekwaksd--nfttvesIECPDDNTVVMNLkdtdvSIITKLswygtFIMPKHLYEgtd---qtrNEY 186 Holdemania filif...
ZP_03635356 124 TSADVKWTYDTAIAekwskad--nlsnidsIECPDDNTVVMNLktpdvSIIAKLawygtFIMPKHLYEgtd---tatNPY 198 Holdemania filif...
ZP_03635358 122 TSNDVVWTFTKVLEegyqsnt---lnmidsVTADGDYKAVFHLkqpdaSVVSVLswlgtWIMPAHLYEgtd---wtqNEH 195 Holdemania filif...
ZP_03635359 122 SSEDVKWTLDMIRTegfqsns---fkmieeITCPDASTVVIQMsspsaAILSSLgwlgtFILPKHIYEgtd---wtaNDA 195 Holdemania filif...
ZP_03635381 121 SSEDVKWTFDKIRTegyqsns---fkqlseITCPDENTVVFHLsepnsGIVATIgwlgtFIMPKHIYDtpdy-dwstNPA 196 Holdemania filif...
ZP_03635351 118 TSEDVKWTFETMKEyswtksd--slaavtsIECPDENTVVLNLsqrdvGIVPKLgwyatFIMPEHIWNdpaysdfvsNPA 195 Holdemania filif...
ZP_03635353 116 TSADVKWTYDTLIAekwnksd--slasvesIECPDDNTVVMNLkypdvSLIAKLswygmFIMPKHLYEntd---tatNEY 190 Holdemania filif...
ZP_03635354 120 TSKDVKWTYDTIIEnkwsksd--tfvnvdtIEAPDDLTVVFNMknpdaGLVPLLawyatFILPEHIWNdpaypdfakNPA 197 Holdemania filif...
NP_142742   196 LNKPIGCGPFKFVEWVKGDHITLVANENYFrGRPGIDKIIYKIIPDAsaalqAFLAGeGDVLGqrpplteipRLKSTPg- 274 Pyrococcus horik...
NP_971012   194 KEKPIGSGPFKLLKFKQGESVTLEANKNYFmGAPKIDNVIFTIIPDSatavqALVNGeIDVLEnipa-annrELLANPq- 271 Treponema dentic...
ZP_03636508 187 NQHPVGTGPFKFVEHKKGVSITLERNDEYWgDTPILDKIIFSIIPDEmtayqAFLQDeVDYLGtgvpstntnDFDDNP-- 264 Holdemania filif...
ZP_03635356 199 NQNPVGTGPFKFVEYKAGQYVTLERNEDFWgDKAIAKTLKFAIISDDntlweAFMNGeVDDLCqmipaahanDLDGNDny 278 Holdemania filif...
ZP_03635358 196 NMHPIGTGPFKFVKYTPGVSIEMERNEDYWdGAPYLDKLIISIIPDAstayqSYLNGeVDDMQsgvptsdlqELIDDPe- 274 Holdemania filif...
ZP_03635359 196 NMHPIGTGPFKFESYEKGQAITLVRNDDYFmGAPYLDKLVITIIPDAntafqAYMNGeVDDLMlnipsneiaGLKANPd- 274 Holdemania filif...
ZP_03635381 197 NFQPVGTGPFKFVSYEKSVAIRMERNEDYFkGAPYIDELIVSIIPDEstafqAWQNGeVDDILgkapsseiaALKQDP-- 274 Holdemania filif...
ZP_03635351 196 TWNPVGTGPYKFEKYDAGVGTTLVRNEDFFgTKATIEKLIFQVIPDQttayqSFLNGeVDYLGvtvptankhELDNDP-- 273 Holdemania filif...
ZP_03635353 191 NMKPVGTGPFKFVEFQKGVRVVLERNEDYWgDKAKVAKVIYSIIPDAttayqAFRTGeVDYYTaips-qnanDFDNDPdy 269 Holdemania filif...
ZP_03635354 198 MQKPIGSGPFKFVEYKSGQSVTLERNEDFFgGAPEIERLIYQIMPDLnttleAFKNGeIDYITslpt-anlhDFDNDP-- 274 Holdemania filif...
NP_142742   275 vSVSIRPVp--sRWYLGFNlkrp-ylqDVRVRLAIAYAINRKELVEKAEnGLGYPaegTYVPAIKWAynpn---aklPEY 348 Pyrococcus horik...
NP_971012   272 lRLVFNEYp--sPMRIIFNmrne-kvkDVNLRRAIASAINKKEISDKIFdGVQKPe-yAMYPQFIKWvsnt--envsPQF 345 Treponema dentic...
ZP_03636508 265 -DYEVYLQlsmnRLYLAFNfede-hfsKPEVRKAVAMGVDRQMIYDRVAnGVGGVaetFISPMAEDFaddr---ytmPEH 339 Holdemania filif...
ZP_03635356 279 tFYSEMGIn---RTYITFNlkde-rfqDQRVREAFALAIDNQGCWDRTAgGNGEPseyMISHAFTKYlded---sklPKR 351 Holdemania filif...
ZP_03635358 275 -HYNVYQYvsssRTYLSFNigednpfhDVRVRQAVDLAVDRQAVLDKAAkGFGAVseyYISPMYPWAlndd---akiPSR 350 Holdemania filif...
ZP_03635359 275 yTVYERASn--nRTYLTFNfdee-pfnDVRVREAVNLGINRQEVLDKAAkGIGAV---PKYYMTPVFawamndavtiPER 348 Holdemania filif...
ZP_03635381 275 -NYNVYQYvatgRVYLSFNlkeg-pfaDVRVRQAVDMALDRQEILDKAAkGIGSV---PETYMTPVFdwamsetariPDM 349 Holdemania filif...
ZP_03635351 274 -NYKHFHYlsinRTYITFNmets-ifkDVRLRQAVAMGVDRQGIYDRVAnGTGALaeyFISPLWEGKyldk--qytmPAR 349 Holdemania filif...
ZP_03635353 270 eVYPVIGMn---RSYVTVNmtnd-tfkDARVRQAIAYGIDRQMIWDRCAgGTGAVastFIAPNTGFAdek----yqmPER 341 Holdemania filif...
ZP_03635354 275 -NYEVFSFlsinRTYLTFNmeke-pfnNPKLRQAVAYAVDRQAIVDRMGnGVSALpeyFISPLFEDYlndd---yklPER 349 Holdemania filif...
NP_142742   349 NPEKAKQLLDEAGFkdingdgfretpdgkPLELRLLYFTGSDtNAICTLIKEQLAKVGLKVKLEsyEIATWEQKVVKerD 428 Pyrococcus horik...
NP_971012   346 NIDAARKILQDAGYkadk-------dgffVRGLQIEVFEGGGyPDAAKLMQATLAKAGIELKVNvsEYNAWSDKVGAnrD 418 Treponema dentic...
ZP_03636508 340 NVEQARKLLEQAGYtana--------dgyYFSMEFSVFENGNyKEIAEIIQQNLKEIGIDMRINmmDYAIWTEKVKQnkE 411 Holdemania filif...
ZP_03635356 352 NVEEAMKLLEEAGYtkda--------dgyYMHVTLDAFESGNwKDLAAIIQQNVKEAGIDLKINmmEMAAWQDKVQVnrN 423 Holdemania filif...
ZP_03635358 351 DVEAARKLIEDAGYtada--------ngiYFSCELTTFDSGDfKDSAIVIQDSLKQVGIDVKLNvlEMGAWMTKVIDdyN 422 Holdemania filif...
ZP_03635359 349 DVEKARQLLEEAGYtada--------ngmYMSVTLDLFDSGDfKDTATVLQQNLKEIGIDVKLNitEMGTWQQKVQVdsD 420 Holdemania filif...
ZP_03635381 350 DWEAAKKLIEEAGYtqde--------ngyYFTCTLDTFESGNfKDTATVIQAQLKEIGIEVKLNisEIANFQTKVLDnyN 421 Holdemania filif...
ZP_03635351 350 DVEAAKKLIEEAGYtlrd--------dgfYFDMTMDIFESGNfKDIAQIVKENLKEIGINVTLNimEMAAWQDKVITnsN 421 Holdemania filif...
ZP_03635353 342 DVAKAQQLLEEAGFkkda--------ngiYFSTEMKFFESGYfKDAATIIQSNLKEVGIDVKLTmlEYAAWVDNVKVnhD 413 Holdemania filif...
ZP_03635354 350 DIAKAQALMEECGLkkns--------dgyYLTVTLDAFENGNfKDVAAIVQSSLKEAGIKVELNlmEYAAWTDQVKEgrK 421 Holdemania filif...
NP_142742   429 FDLALVDGfqgpDPANMEIRFKStayiNFAGYNNTEFDKLLEEAAkttDTEKRKELYWKAQEILAKdLPYLPLVDLv-aI 507 Pyrococcus horik...
NP_971012   419 FMLELQGGfmgpDPAALYSRYGTdesnNWSGYSNIKFDELCKKGLtvgNKEERAAIYKEAQKILAEdLPFIPIVGF---A 495 Treponema dentic...
ZP_03636508 412 YQMTMSAGyqgpDVSGIAGRVSThgsnNFMNFSNARLDECLEEALktsDHETRKAYYSEVQKIMSEeMPMAILLDNg-vK 490 Holdemania filif...
ZP_03635356 424 FEITMLAGyqgpDISGVSGRVQTgtsmNMAGYSNPELDALLDKGVtlsNEEERIECYKEIQKIMRAdLPIIPIIDNg-yK 502 Holdemania filif...
ZP_03635358 423 FDIALCSGgqgpDVSAIRNRVHSegslNLTKYNNPALDEALNEGVkvfSEEERAPYYKEAQQIMHDdVPIVILKDF---T 499 Holdemania filif...
ZP_03635359 421 YQMAMLSGsqgpDASAISMRVHSagafNLAHCKNAELDALLDEGAittDQAARAEIYKQAQVILAEeLPIVPVKEAt--F 498 Holdemania filif...
ZP_03635381 422 FDMAMNSGsqgpDANAIENRIGSngslNISKYANPEIDELLKQGIavsDKAERGEVYKQIQEILKRdLPMVIVTDEi--Y 499 Holdemania filif...
ZP_03635351 422 FDMTMLAGyqgpDVSGVAGRVASnggtNVGLYNNPEMDAALQAGVetdDDAERAKAYSEVQRLMSEdMPMVFLFENgdcL 501 Holdemania filif...
ZP_03635353 414 FEMTMAAGyqgpDVSGISGRVGTgtsmNFMGYSNPELDALLEKGVqisDETERKAVYSEVQRIMSEeMPIILFMDNg--A 491 Holdemania filif...
ZP_03635354 422 FNMTMLAGyqgpDISGIYMRVGItgsnNFTGYASDVMEAALEKGAqnsDPAIRKEAYDEVQRLMSEdMPMVLLLDNgqvI 501 Holdemania filif...
NP_142742   508 SVWRS------EFHGM 517 Pyrococcus horikoshii OT3
NP_971012   496 SYDANs----vNFKNL 507 Treponema denticola ATCC 35405
ZP_03636508 491 TPIKK------YLSGV 500 Holdemania filiformis DSM 12042
ZP_03635356 503 YAIKK------EMKGM 512 Holdemania filiformis DSM 12042
ZP_03635358 500 AVYPVk----sYIHNS 511 Holdemania filiformis DSM 12042
ZP_03635359 499 TVAVRn-----TIHGH 509 Holdemania filiformis DSM 12042
ZP_03635381 500 SYPIKa-----TIHNH 510 Holdemania filiformis DSM 12042
ZP_03635351 502 PVAANld---gTPRDV 514 Holdemania filiformis DSM 12042
ZP_03635353 492 KVPVKk-----ILKGT 502 Holdemania filiformis DSM 12042
ZP_03635354 502 PVKSKfdgtpyQVPDK 517 Holdemania filiformis DSM 12042
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