Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_5

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cd08511: PBP2_NikA_DppA_OppA_like_5 
The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold.
This family 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: 173876
View PSSM: cd08511
Aligned: 19 rows
Threshold Bit Score: 603.502
Threshold Setting Gi: 121607928
Created: 27-May-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_889056     26 QDLRIGLqeDPDVLDPHRar--tYVGRIVFts--lCDKLVDIDekLQFVPQLAQSWSFSe-DNKTLTFKLRTDVQFHDGS 100 Bordetella bron...
YP_001359900  54 GDLVMALsaEPDRLDPTTss--sLYTRYVMna--iCEKLYDVDagGNLVPQLAAALPTTspDGLTVTIPVRPGVRFADGT 129 Kineococcus rad...
NP_355946     24 SELRIGLndDADVLDPAQsr--tFVGRIVYta--mCDKLVDISqdMKIVPQLATEWAWSe-GGKVLTMKIRDGVKFHDGE 98  Agrobacterium t...
YP_001103524  48 GEAVIALdqEPDRLDPTLat--tLAGRQVFag--lCEKLYDVDqaGRIVPQLATELPRAsaDGRELTIPLRPGVRFNDGT 123 Saccharopolyspo...
YP_553371     37 GTLRVAFtsDTKTLDPTFsv--nFSERQPLyl--iYNTLLSINpdASIGPELAERWEILg-GGKRLVLHLRKGVVFHDGT 111 Burkholderia xe...
YP_998579     44 GTLNIGVeaDPASLDPLRlg--sYVERQYAma--vFDTLLDIDasGKLVPSLATAYEISp-DGRAYTLKLRQGVTFHDGT 118 Verminephrobact...
YP_994923     30 GTLTIGMeaEFSGFNPAKar--iFNQNTLApassvLETLFVFEg-AQIVPRLGLDYAEAp-DRLSATVRLRPGVTFHDGT 105 Verminephrobact...
YP_001229966  46 GTLTVAVeaDGRGFDPIKagflsSQARSVAma--iEERLFDMDakGKLVPELGLSATPSk-DGKTWTIKLRKGVSFHDGI 122 Geobacter urani...
ZP_04039503   20 QTVTVGLdaDPPNLDPLLss--aLVDRQVQnq--iYDKLVDLDenLRIVPMLATSWRVEe-DGKVYVFNLRQGVKFHDGT 94  Meiothermus rub...
YP_002787509  24 QTLTVGMdaDVVRLDPVLs---aAAVDRHVly-qvFDRLVDVDenLKIVPSVARSWKISs-NGLTYTLTLRSGIKFHDGT 98  Deinococcus des...
NP_889056    101 KFDAAAARANLERAMTLqd-smRKGELAsv---ekIEAPDPATLVLTLKrp--dATLLAQLSDRAGMMLSPkafegda-a 173 Bordetella bron...
YP_001359900 130 PLDAAAVVTTLERNLTLet-ssRKSELGpv---rdVEALDPATVVVHYEtp--fAPLTASLADRAGMVMSPtalaerg-e 202 Kineococcus rad...
NP_355946     99 TLDAAAVVATIERNMTLpe-srRKSELSsv---ekVEATGPLDVKFTLKtp--dVTLLAQLSDRAGMIVAPkaakelg-a 171 Agrobacterium t...
YP_001103524 124 PFDAAAVKRSLDRHRELdg-ssRRVELSav---asVEVADPATVRLRLTtp--sAPLPSVLADRAGMVMSPaqldrlg-e 196 Saccharopolyspo...
YP_553371    112 PFDAAAVKTNIDMRLDPavsspLRPQLAliv--dnVQVNDPATVTLNLKsp--sPALLGMLAQREGFMASPaamrkyg-k 186 Burkholderia xe...
YP_998579    119 PFDADAVVYNLDRVRDPv---nNCRCLAnissvesVKAVDTHTVVVRLQap--sVAFAALLADTAAMMASPkalkadp-v 192 Verminephrobact...
YP_994923    106 PFNADAVVAHYAWLLAPgt-giNLSPIApl---ktVEKVDEMSVRFVLRqpwvaLQSALAAENLVNFIGSPaalkndp-e 180 Verminephrobact...
YP_001229966 123 PFNADAVVQHWERLLDPk---nRFRGLVtmqpiesVKKVDDFTVRFQLKhv--wVPFKDVIASTNGIAAYIpspkamkeg 197 Geobacter urani...
ZP_04039503   95 DFNAEAVKFNLDRYRSApg-srRSGELSli---tnVQVVNPYTVRVTLRep--fAPFLAILSDRSGMMVSPtavqklg-a 167 Meiothermus rub...
YP_002787509  99 SLNAAAVKYSLERSLNMdg-saRKNELSai---ksITAVNPTTVRIDLHap--fGPLLAILSDRAGMIVSPtaaaksg-a 171 Deinococcus des...
NP_889056    174 avgrkPVCSGPYKFVERVQNDRIVLQKFDQYYgakDYHFDKLVFLPIPDtTVRLSNLRAGglDILErm-nPSDApqvknD 252 Bordetella bron...
YP_001359900 203 dfgdhPTCVGPFRFVERVPQTSITVERDPGYYaadRVHLDTITYRIMTDaNIRAANLRSGdvQVADtl-sPQDVdalaqE 281 Kineococcus rad...
NP_355946    172 nfgskPVCAGPFKFVERIQQDRIVLEKFADYWdkdKILVDKIVYLPIPDtTVKLANLRAGdlDIAEri-sASDAesvknD 250 Agrobacterium t...
YP_001103524 197 nfsdhPVCVGPFEFVERVAQDRIVLRRSDFYYgrdHVMLDRLVYRAVPDdNIRLANLRSGefDVVWea-gPPEVpilarD 275 Saccharopolyspo...
YP_553371    187 dfgthPVGTGPFVFKEWIPGNSLTVEKNPHYWepgKPYLDRIVLSDTSNpIVAMQRLRTGevDYISal-sPIDIrpiekQ 265 Burkholderia xe...
YP_998579    193 gfgnvPVGTGAFKLVEWVKGSRFVGERNPNYWrqgQPYADRLIYRGLQSnETRESTFQSGalDILTqa-sPKFVaaakkD 271 Verminephrobact...
YP_994923    181 gfhrkPIGTGPFIFKEWQAGDRIVMERNPHYWepqLPYLERLIYRVLPDaNTRYQSIKSGqvDIGRmd-tASHVldarkN 259 Verminephrobact...
YP_001229966 198 tqdlaPVGTGPYKFKEWIANDRLVVVRNPSYWrkgKPFLDSVVFRTVPDmQTRFAGLKSGelDVILtdrgASILqa-reD 276 Geobacter urani...
ZP_04039503  168 efgnnPVGTGPFKFVERRRQDRIVLARNENYWqrgFPRIEQLIYRPFPDdDVRVANLLSGavSIITpv-aAKDLatirnN 246 Meiothermus rub...
YP_002787509 172 dfgraPVGSGPFSFVSRTQQDNITLNSYSEYWn-gAPKIDKLVYRPFPDgDVRYANLLSGgaQVIVv--dAKDVeklesN 248 Deinococcus des...
NP_889056    253 ASVQFMPVSGlGYQEVFFNtgngkra-------etnpfkDKRVRQALALSIDRAIINEVVGgGIFDPasqpfPPASPYHs 325 Bordetella bron...
YP_001359900 282 EGIGLLQTGSfGYQGITFNlgntdgvgkppgridtplatDPRIREAFSLAVDRTALVNSVFnDWYEPacsfvSPASTYAt 361 Kineococcus rad...
NP_355946    251 PKLTYADVIGpGYMAMYVNinngara-------dnplgkDKRLRQAFSYAIDREAIGQIVFeGTSKAgnqsfPPTSPWFn 323 Agrobacterium t...
YP_001103524 276 SDVVLLNTPSvQYMGITVNianvggstg---pvpgplaaDPRVREALSLSIDRATLNKISFnGLYRPacgpiPPTSEFAt 352 Saccharopolyspo...
YP_553371    266 PGIVLDPGPAsRWYALQWQidrp-------------pfnNPLVRQAVAHAIDRKRMVEILMnGKVPIsdsiaPPGTWWFd 332 Burkholderia xe...
YP_998579    272 RRFKVLEPDGfGSIFIALRtkhp-------------alaDMRVRKAIAHATQRELLVKAVYqGMYKVat--tPFGEGLPg 336 Verminephrobact...
YP_994923    260 PQIKVHEYQGsGAISWNFNaake-------------pfnDQRVRAAVVHAFNAKAMLDTFFlGTTVAttdlfGPNSPWFc 326 Verminephrobact...
YP_001229966 277 RSLKVYSSDAtGAETFIFNtskp-------------plnDVRVRRALSYAWNQEFYIKASYkDTIAVar-dpFGGTIACg 342 Geobacter urani...
ZP_04039503  247 PNLTVNNFPGiGYQGIWLNhtkg-------------pftNKALRQAFAATIDRDVVDRVVFlGTALPsngpfPPGTLAYd 313 Meiothermus rub...
YP_002787509 249 NKFNVISIPTlGFQGIWLNttra-------------pfnNKLVRQAVAATIDRNAVAQVVFrNTAKPaagpfPPNTPAYs 315 Deinococcus des...
NP_889056    326 dk--fpvPKRDVERARALLKQAGLqkvkaEFAFGNNTt--tSAIAEMIQAMAAEAGFELSLRptEYAAMLNEAQAGNFEM 401 Bordetella bron...
YP_001359900 362 aas-dacPPHDPARAKELLTEAGVel-pyRITVSASNtadtLRLSQALQASVLEAGFALEIEpvEYSTLLDQQSSGDFEA 439 Kineococcus rad...
NP_355946    324 qn--lpvPTRDIDKAKQLMKEAGYet--lDVELQHANnttqTQMMQVIQSMVAEAGFNVTLKatEFATLLSEQTAGNYQL 399 Agrobacterium t...
YP_001103524 353 prt-qacPPHDVGRARRLLAEAGVrt-plRVELMLANdsaqNRTGQVIQAMAARAGFDVVLRptESTSAIAAAKKGRFET 430 Saccharopolyspo...
YP_553371    333 ps--vhsYPYDPAKAKALLAQAGVtn--lSVGLSTPQimllQQINQLVQEQLKAVGITVRLDpiAQSDWYPRVSQGLVNF 408 Burkholderia xe...
YP_998579    337 lspvtdyPAYDLDKAKALLAEYGQa---vELRLMMDNtpiaLQAAQALQQMWQRAGIKVTLTpvDQARLVQNMLTHEFDT 413 Verminephrobact...
YP_994923    327 pr--lnwRSHDLAKARALLAEVGKp---vKFQLVSTNtptgRRQAGMVQQFAKEAGMEVDIRltEQSQNVRVGLSGDYQM 401 Verminephrobact...
YP_001229966 343 dl---gyRGFNPEKGRQLIAEYGKp---vNLELQITNtprgREFGEIVQRLYKEIGVTVTVTplTLGQRNKKVFAGDYQM 416 Geobacter urani...
ZP_04039503  314 kt--ipvPRRDLALARQKLAEGGRpq-gfSFTLTIAPgpvlAQLAQVYQAMAAEAGIQVRIEqvEFGTLLDRAAKLELEA 390 Meiothermus rub...
YP_002787509 316 ss--ikvPTPNIADARKKLKQAGVsn--lTFTMIAATgtttALLTQVYQAMMAEAGINMKIElvDNGALSSRATSFNFDA 391 Deinococcus des...
NP_889056    402 IMRGWSGRv-DPDGNIYQFVtck-----galNDGRYCNAEVDKLLAEARtvpDQAKRKVIYDQAQALLQAdTHDIYLYYQ 475 Bordetella bron...
YP_001359900 440 VQLGWSGRv-DPHGNSASFLtta-----agnNYSGYSNPEVDALLKQAArstDPATRADLYGRVVTLVQRdDPIVYLYRV 513 Kineococcus rad...
NP_355946    400 SRSDWSGRi-DPDGNLHQFVtck-----ggiNDVKYCNPEVDKLLNEARastEDAVRKEKYDAASVILNDdMPIIYLGHQ 473 Agrobacterium t...
YP_001103524 431 FLIGWSGRp-DPDGNIAVMHteg-----spqNYSGHSTPETDALIARAAaeqNPDRRRGLYELVVEDLHErNNVIYLYRQ 504 Saccharopolyspo...
YP_553371    409 TPMRWAQRp-DPDGLFPLLFgst-----gaqNSTKYKNPEVDRLLEVARnsaDQSERKAAYGQIEAIVTRdLPYVPLFFS 482 Burkholderia xe...
YP_998579    414 TLFRWSGRp-DPDLNAYTFFhssnaekkissNYIQYANPEMDRLLDAGRmemDPSKRNQIYNQISQLLAKdLPYVFLAYI 492 Verminephrobact...
YP_994923    402 GVWRFGDItgEPDGALAYYFgge-----ngtPVSRHDTARIDALLGKARaepDQARRKALYCDIAQIVSDeAYQLIPIRV 476 Verminephrobact...
YP_001229966 417 TGWQLFDAt-DMGPTLYANLysk-----seiNFSQYRNPEMDKLLTTLQisaNNKERQKALCGVAKQLNDeAVFLYRGAI 490 Geobacter urani...
ZP_04039503  391 VAVGWSGRp-DPDGNIYDFVrck-----apnNYSGYCNPRVDNLLNRARtvrLPEARRDLYSQITKIIQEdLPYIYVYHP 464 Meiothermus rub...
YP_002787509 392 ALLNWSGRi-DPDGNIYDWVrtg-----gtyNYGRYSNKEVDALLAKARaqsSMSARKATYNVALGKVLSdTPYIWVYHQ 465 Deinococcus des...
NP_889056    476 p---wPFVLGK-NVRGFkpyPDGMVRL 498 Bordetella bronchiseptica RB50
YP_001359900 514 rsitgYVSSGDdAVAGIetyADGVVRL 540 Kineococcus radiotolerans SRS30216
NP_355946    474 p---yAYAISN-KVKGWapsPDGMIRL 496 Agrobacterium tumefaciens str. C58
YP_001103524 505 q---yYTAHSA-DLAGVavyPDGIMRM 527 Saccharopolyspora erythraea NRRL 2338
YP_553371    483 l---eYAAMRT-NVHNHvwlPDEIPRF 505 Burkholderia xenovorans LB400
YP_998579    493 t---aPIVTTQ-AVRGVelvPDSLIRV 515 Verminephrobacter eiseniae EF01-2
YP_994923    477 t---yYAIASP-KVRNLgpiTNSIIRT 499 Verminephrobacter eiseniae EF01-2
YP_001229966 491 r---ySAIAKA-GIQGIskvDHGIVRV 513 Geobacter uraniireducens Rf4
ZP_04039503  465 q---tTIGVSR-RLSGLpviPDGILRF 487 Meiothermus ruber DSM 1279
YP_002787509 466 s---nMYGTTK-AVSGLksiPDGILRF 488 Deinococcus deserti VCD115
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