Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_7

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cd08512: PBP2_NikA_DppA_OppA_like_7 
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: 173877
View PSSM: cd08512
Aligned: 99 rows
Threshold Bit Score: 299.128
Threshold Setting Gi: 15899344
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_106164     88 PADTLVEGFaiddiiSMDPGEafelsTAEVTgNTYDLLVRLDlsdtSKVKPD--LAESWTVSDDg------lTYTFKLKP 159 Mesorhizobium l...
NP_228270     22 NPDTIIDATige-pdTLDPHFaydtaSGEVIyNVYENLIAYKgeslTEFEPR--LAERWEILDDg------kTYKFYIRK 92  Thermotoga mari...
YP_001737522  61 NPDKLIEATige-peTLDPAWaydtaSGEVIfNMYETLIFFDresvDKFVPM--IATQVPSFENglikdngtTIIFPIRK 137 Candidatus Kora...
YP_684666     39 TSPMTIVSMvagepeSLDPAYdyesaGGEIIqNVYETLVYYEg--dDVTKPVgvLAKSWEMSEDg------lTYTFYLKE 110 uncultured meth...
NP_147134    270 HPDTIIVARige-pqGLDPAFahdtaSAEIIdNVYERLVWTTkn-fKEIKPW--LAERWEIKDNg------tTYIFYIRK 339 Aeropyrum perni...
NP_294710    103 NPDTLVVQEsad-ipTLDPGTtydtaSGQVVeNLYETLLGYQgnsiRDLQPI--LATKWEEEDGg------kRYRFTLRD 173 Deinococcus rad...
NP_294086     32 PKDTLVLQYsad-vpTLDPGVsydtaSGEMIeNMYETLLTYKgsslKTLEPL--LATKWTASNGg------kTYTFDLRK 102 Deinococcus rad...
YP_002508243  27 NPDTYVHVTigd-qsTLDPHYsydtgSSELIyQVYETLIDYKgssvTEFKPL--LSTKVPSVENglikdggkTYIFPIRQ 103 Halothermothrix...
YP_002830417  73 PSSITVEEAat--pvSVDPASsydiaGGEIIqNVYQTLVFYNgtntSSFIGV--LAENWTVENNg------tTYIFHLWP 142 Sulfolobus isla...
YP_001541144 108 PSELIDVSQvaa-pdCLDPATgfyvqDGPIFaVVFQGLVGFNgsnyMQIVPV--IAKNWSTPDDq-------HWYFTIRH 177 Caldivirga maqu...
NP_106164    160 gLKFASGNPITAADVAYSFERAVKLDkspafiidqf---------------------------------gisgdnvtekA 206 Mesorhizobium l...
NP_228270     93 gVKFHEGGDLTPEDVEYSFERGLIFDptagpmwmlwealfgvdsletfveekigkpyselfdengeplpeyrdalikiyT 172 Thermotoga mari...
YP_001737522 138 gIKFHSGRELTPEDVEYSLERVLVMDrdggpswmlldpllg------------------------vqstrdekgniivsF 193 Candidatus Kora...
YP_684666    111 nVTFHDGTAFNASAVKYSFDRGVIMNldpwqscispllaggldy-----------------mnsnqteadqkayldldsV 173 uncultured meth...
NP_147134    340 gVKFHNGEELTAYDVEYSFKRLLVLDlpqghvrqikpfl----------------------------idewdpdqidqaI 391 Aeropyrum perni...
NP_294710    174 gVKFHSGNPFECKDAEYTFRRNLVTNtsdsgnwflsesll-------------------------gtasnanddkgvtwQ 228 Deinococcus rad...
NP_294086    103 nVKFHSGATMTCTDAEYTFERNLVTNsgesgnwfiaepll--------------------------gtqnnanddksvtW 156 Deinococcus rad...
YP_002508243 104 gVKFSNGNPLTPEDVEYSFERALILDraygpiwmfyeplfglgslsdl----------tkkvvgvedpkkltpeqsakvY 173 Halothermothrix...
YP_002830417 143 fITFSNGNPLNATDVWFSIYRTMLINlgisiytsqalavnnglgf----------------vgklpngkygtimlpngiL 206 Sulfolobus isla...
YP_001541144 178 hVWFSNGDPVNATTVWFSIYRTILMGqgpgisnygnilynitkatltgyfi---pwgachalayatgnnaylsnatlcaY 254 Caldivirga maqu...
NP_106164    207 KAID--------DTTFQFTVdkay---------apsFVLNCLsat----------vaSVVDAKLVkehvaavtp------ 253 Mesorhizobium l...
NP_228270    173 DYIDpai--eveGDAVVFHLvrp-----------faPFMYILaqsa--------swsAVLDKEWCieigcwdgra----- 226 Thermotoga mari...
YP_001737522 194 EDIDkav--evqGDSVVLHLkkpy---------pitTLFQILsqt----------wsSIVDKQCAiahgdwdgt------ 246 Candidatus Kora...
YP_684666    174 HVVN--------ETTVQFKLakp-----------ygAFVPVLsfy----------aaSIISPTYDqahg----------- 213 uncultured meth...
NP_147134    392 RAID--------KYTVVFKLkkp-----------faPFLRILasd---------yafVIINKKWAiehgdwdpsl----- 438 Aeropyrum perni...
NP_294710    229 KIVDavk---cdGQTLVFNLpkt-----------dpAFLSKLayt----------gqGIVDSEHAkkigewdgte----- 279 Deinococcus rad...
NP_294086    157 DKIDkave-cnsKGQLVFNLakv-----------dpAFLAKLays----------gqSIVERKYNasigewdgte----- 209 Deinococcus rad...
YP_002508243 174 AEIDkki--evdGNNVVFHLenp-----------ypPFLNILakga--------swaSILDKEWSieqgawdgsp----- 227 Halothermothrix...
YP_002830417 207 QALEsagynfssNKTIAMEQaaydlayilshfnvsnTTIQKVmsyp-------hqavVVIDPYTVefnldypysaflaal 279 Sulfolobus isla...
YP_001541144 255 ALANvlsnfnvaNATIQKIMsypnqai--vvlnpfeVEITTLkpyplflsdiaawwgFVVDPVFIdshg----------- 321 Caldivirga maqu...
NP_106164    254 -------------sadykwdnDFGNAWLk-tGYAGSGAYKLREWRAn-EAVVMERNDNYHg------------eKAKLAR 306 Mesorhizobium l...
NP_228270    227 ------------dtwwkyhdiRKEDSPLy-aRMNGTGPFKFVEWDRaqQKVILERNDNYWr------------ePAKIKR 281 Thermotoga mari...
YP_001737522 247 -------------eknwtkynNPENPPLq-eADCGSGPFMLDRWEHg-KQVVLKKFDQYWr------------gPANFSE 299 Candidatus Kora...
YP_684666    214 -----------------gykaNEESEWMt-sHMCGTGPYVLTSWDRk-DKIVLDKFDNYHg------------tPAANDR 262 uncultured meth...
NP_147134    439 ------------pksewskfrGKINDYIm-rNPMGTGPYKMVEWVPg-QRIVLERFEDYWq------------gPAPTKR 492 Aeropyrum perni...
NP_294710    280 ------------atwkaavgkDLTGSPLa-qDPSGTGAYKLLKKDA--TSVAAVAFDDYWg------------dKPSIKN 332 Deinococcus rad...
NP_294086    210 ------------ktwktwvgkDLTGSNLs-kKPNGTGPYRLVKQDA--NNLLFQAFDGYWg------------kAPSIKN 262 Deinococcus rad...
YP_002508243 228 -----------etiakyhdpvKEDDPLFn--KMMGTGPFILVEWVNg-DHVIFKRNDNYWr------------ePANFKT 281 Halothermothrix...
YP_002830417 280 ststgaivnpvfvdenggvqiDTSNTYLs-tHALGSGPYILETPIGg-SYVVLNASPNYWaskvptkdlnpmleTPKIKT 357 Sulfolobus isla...
YP_001541144 322 -----------------gvqpNTPNSELcttPMPGTGPYIIKSYTPg-EELLLVNNTDYWvyyyy-----nhgmASEIPW 378 Caldivirga maqu...
NP_106164    307 VIYRNmkessAQRLALEAGD-----IDVARNLepndlda---------------iaknadLTTT---SAPKg----tVYY 359 Mesorhizobium l...
NP_228270    282 VIIWGidewsTRRAMFLQGD-----ADICAVPtqyleq----------------vegkpgVTVVk--GLPEla--vtSLH 336 Thermotoga mari...
YP_001737522 300 FIIMKvdewsTRKLMFLRGD-----VDIAYVPrqnmke----------------vegepgIRIIk--NLPTvt--ndALF 354 Candidatus Kora...
YP_684666    263 VIIRYvddwnTRFLAIKNGE-----ADLIYAPttyadd----------------ikkepnLVLEt--GRGTl----sVTY 315 uncultured meth...
NP_147134    493 VVIMFvpelsTRLLMLKNGD-----VDIADIPvsyksq----------------venvpgITIFt--GAATn----vVEF 545 Aeropyrum perni...
NP_294710    333 VIIQKvpepaARIQAFLKGD-----ADFIEAGgreivet--------------qlkgkpgVAVLd--DLPDt----tATG 387 Deinococcus rad...
NP_294086    263 VIRQKvseiaPRQQAFLRGD-----ADVIEGGgrnvdea--------------qikgkpgVAWLd--NLPNts--afVIF 319 Deinococcus rad...
YP_002508243 282 VIIKNvdeptTRILMLKRGDa----DSISLDYqyfnqi-----------------egvegIKITr--GIPVlqnmtmLFN 338 Halothermothrix...
YP_002830417 358 IIIDYqtneaVRILDLQQEKaqisqIDVIDLQeligssgvqqlqnlvngktfptaytsgnVTIYi--WGPSa----qIDF 431 Sulfolobus isla...
YP_001541144 379 IIQPAhityiDVKYGLDTTDr---iEDFVKNIaqittvstitmpelvklyssatgipsgnWSLYihnFGPSg----cVFY 451 Caldivirga maqu...
NP_106164    360 ISLNqknp-----------------------nlaKPEVRQAFKYLVDYDALSSTILk-GIGEIhqsflpkgdl-----ga 410 Mesorhizobium l...
NP_228270    337 FAWNvpedskyigsgk------ldgngippdffsDENVRKAFIYAFDYDTFINEVLk-GLGRKiptdlpegllgfneell 409 Thermotoga mari...
YP_001737522 355 FNFNisptspyigsgk------ldgegippnffqDKNVRLAFVHSIDYDKYIEEAWf-GEAIRtpgpipqglp----gyf 423 Candidatus Kora...
YP_684666    316 IGFNqkek-----------------------vfqDQRVRQAFIESFDAESYLKDVCl-GYGKRvngpipeglp----gfn 367 uncultured meth...
NP_147134    546 IQFNfniskipeg------------dtiwpdfftDVNVRKAFAYAFPYEEFIEKAYq-GLAIRaracvppgwp-----gy 607 Aeropyrum perni...
NP_294710    388 LSMNenikvkagqeqqqigsgkldgngipanffsDVDVRRGFVAAFNTPEYIKQVQr-GKGTErnfllpdsfp----gyd 462 Deinococcus rad...
NP_294086    320 MNQNikatnllgsgkl-------dgngipanffrDANLRRAFSYSFNYQQYIDDVQk-GKGKQrtmalpdsfp----gyd 387 Deinococcus rad...
YP_002508243 339 WDINskgneyigsgkl-------dgngippdfftDVHVRRAFSYCFNYEAFIEQVRd-GQSMKlrgpivspll----gyd 406 Halothermothrix...
YP_002830417 432 LAIDayqy-----------------------pfnITAVRLAISHAINPVQIQQQVYk-GFAINyvgpldpslp----yyn 483 Sulfolobus isla...
YP_001541144 452 LSFNnyvw-----------------------ptnDTDFRLAIVHALNATALLQPYYalGMYWAttyvgpiapnfkpyynp 508 Caldivirga maqu...
NP_106164    411 idanpfkLDVAKAKELLAKAGLa----dGFSVTMDVRtgq---------------------ptTGMAESIQQTLGQ--AG 463 Mesorhizobium l...
NP_228270    410 ndpdaphFDIVKATEYFKKAWNgevwkkGFKITLLYNtgn--------------------evrRQAAEMLKAYIEM--IN 467 Thermotoga mari...
YP_001737522 424 kdmpmytFDLKKAEEYFKKAWNgqlwekGFKLTILYNtgn--------------------vqrKTLAEMIKDKVES--IN 481 Candidatus Kora...
YP_684666    368 pdipyqkFDPEHAKALLQEAGFsk--snPTTIVLNYNegn--------------------dnrKQACLMLKDQIEKydLG 425 uncultured meth...
NP_147134    608 veaynyeYDPEKAAEYFKKAWGgrvweeGFVITAFYNagn--------------------eqrRIALELLAESLQK--IN 665 Aeropyrum perni...
NP_294710    463 asipapkFDLDAAKGYFQKAWNgqvwdkGFNLNVSYRsgs--------------------rgmQTAMEMLKKNIEG--LN 520 Deinococcus rad...
NP_294086    388 pkvntytFDKAKATQYFKQAWGgnvwkqGFTLTVNYRags--------------------ttsQTAMEILKRNVES--VN 445 Deinococcus rad...
YP_002508243 407 enspvykLDLEKAEEEFKKAWDgkvwekGFELTITYNagn--------------------marKTAADIFKTYIEQ--IN 464 Halothermothrix...
YP_002830417 484 ssiigytYNPSLSIQLLEEAGFkltlpnGTTVNPNGKpfptitlt----------yqtgstalQDEALLVQQQLAQ--IG 551 Sulfolobus isla...
YP_001541144 509 dnlpvyqYNLTLALQYLVKFLDk----yGYYVVLPNGtaigdtsgtqlptinivtiaplttftKEQFEIIQSELAQ--IG 582 Caldivirga maqu...
NP_106164    464 IKLEIIpg--dGKQTLTKYRARNh--dIYIGNWGQDYFDpn------sNAQTFAsnpdnsdagks-----htlawrnswd 528 Mesorhizobium l...
NP_228270    468 PKFKVEvrgvqWPTYLDATKRGEv--pAFIIGWLADYPDph------nFIFTYYhsagvysgrqgenfrkfvstphpdlg 539 Thermotoga mari...
YP_001737522 482 PKFKIEvraveWPEYLKAMVRGEl--pVFIIGWLADYPDpy------nFVFPYMhssgtfa-------------awqkyk 540 Candidatus Kora...
YP_684666    426 ITIDVQel--dWPTYTAKNRAGEl--pIFYLGWLADYPSadnfigpfcYSEGYYadkv-------------------syk 482 uncultured meth...
NP_147134    666 PKFKLRvqaldWPVYLEKMENFEl--pLFAIGDWINYLDphia--veqQLASYSlfqsl----------------gggys 725 Aeropyrum perni...
NP_294710    521 PKFKVNvvakeWSEIIKASGEGTe--aMVVTSWAPDYADpdnfvntfySSTGYYapri-------------------nak 579 Deinococcus rad...
NP_294086    446 PKFKVKiqpeqWSEMLAASKRGEe--aMVLIGWSPDYADpd------nFLYTFYasdgfys-------------prsnfk 504 Deinococcus rad...
YP_002508243 465 PKFKVNtqvvqWSTFLDQSHRGLl--pLQIGGWLADFPDphnfvqpfiHSQGYYagkrgen-------------yqkwav 529 Halothermothrix...
YP_002830417 552 ITVQLNpe--sAVTIVESYLNPPnssaYPAFQLAGNFPPvls----piDPAIYLlsqarlhh-----------gnpafvd 614 Sulfolobus isla...
YP_001541144 583 VPVSLQl---vTASATDDWVTPSgtpaIVDLGWCPDWPDp-------lFQEMWPltniinggi---------sgnlawfn 643 Caldivirga maqu...
NP_106164    529 IPDLTKETEAAllekDAGKRADMYKDLQQKILDt-SPFVIIHQQleVAGLRK-NLKGF 584 Mesorhizobium loti MAFF303099
NP_228270    540 GRSLDELIEEAiaktDPAERQALYEEIQRFAMKh-ALGMPLYQPl-GVRVQRsWVKGW 595 Thermotoga maritima MSB8
YP_001737522 541 NERVDKLVEELittiDPKKREDICRELTSIYYEd-VPSVIVDQPlgRHYERD-WVHGW 596 Candidatus Korarchaeum cryptofilum OPF8
YP_684666    483 NETIDAIYQEAlyetDPAKQAAMYTEITNGVNNd-AAYIWSTQAv-EFEVHTkQLKGY 538 uncultured methanogenic archaeon RC-I
NP_147134    726 NPKVDELIKQAaletDPQKREELYKQIQLIALRedVPQIYTVYPtvFVVMRD-WIQGY 782 Aeropyrum pernix K1
NP_294710    580 DAQIDSWIKEArsttDTAKRNDLYKKIAERAQEq-ALYILMPGGvgYAVYRD-SIGGV 635 Deinococcus radiodurans R1
NP_294086    505 DASIDKWLNQAratvNTAERNRLYSLVGKRAYEq-APYILVPGGvsYTFFRS-NLVGV 560 Deinococcus radiodurans R1
YP_002508243 530 EVGIDDLIEKGittqDKEEREKIYKKLQQMSHDy-AIDVWIDQPl-SARIERsWVKGW 585 Halothermothrix orenii H 168
YP_002830417 615 NSTINQLIVEAvrtnNPQELQHIYNEITLLTLAq-AQYVWLDDFlaYTVASS-SIHGF 670 Sulfolobus islandicus M.14.25
YP_001541144 644 NSLVNNITNELpfitNLTEQLRLDAEVYKITYNe-APYYWLPTGleYMIVQP-YVKGV 699 Caldivirga maquilingensis IC-167
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