Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_4

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cd08500: PBP2_NikA_DppA_OppA_like_4 
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: 173865
View PSSM: cd08500
Aligned: 56 rows
Threshold Bit Score: 343.454
Threshold Setting Gi: 37522773
Created: 26-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:
YP_001738549  71 PKNPLVVTPvkei----------------gqygGTWRRawygf-------sdkwGPNKICf----------EYPIFRSNd 117 Thermotoga sp. RQ2
YP_143735     25 PQKWTVAKPseakrggtl-------rgytisdyRTFNPflta---------eanSIPDLIn----------PYGLVRRDp 78  Thermus thermop...
YP_001471151  31 DSNPEIGGTlrlalsst---------pesfllyGTLDS----------------AAYTVVmg-------pmFSTLVEMHp 78  Thermotoga lett...
ZP_04034137   19 SAQPKVVSGyeng-----------------kpgGTLTMalssapqtmfyygaidSAIQTLan-------qmFDGLIEYNy 74  Meiothermus sil...
ZP_04040253   17 LAQPKVFKGtepgragga------yritaisdpRTWNPfva----------retSSTDIIsl--------fLPTLTGYSp 72  Meiothermus rub...
ZP_04034134   18 VLAPQMLSKvlaqsgtqanvp-lslfqeigkkgGTLTLplgas-------pqsfNYFSVIdnfaytvlnnvLDRLMQLDp 89  Meiothermus sil...
YP_002787786  19 LAAPKKVSGynalgi------------vngktgGSYTLtlgdspqslfyygvidNNLGLIsq-------qmFDGLVEFNl 79  Deinococcus des...
YP_604808     67 PANQTVAAPsnndmggvl-------rlvqlkdfDTYNPlvaq---------grpNIPELVs----------GAALITPDp 120 Deinococcus geo...
Q9RU24        17 LAAPFVYPAnwtsnkp-----------gdvqtgGTFRSvnlqdfkt-lnpfvssESPNLPav-------lsAGSLLGYNp 77  Deinococcus rad...
YP_002785758  17 LAAPFVWPAawtaeqntapkrggeyrnynltdyKTLNPft------------svEANSLPlrm------gyGTGLFFQDp 78  Deinococcus des...
YP_001738549 118 -gSELVPN--VFESMIVspd-grSFTFKIREgLKWSDGVPVTTEDVRFWYEDILLNeeitpsisad-----lrsggevfk 188 Thermotoga sp. RQ2
YP_143735     79 ttGDWIPY--MAESWTIspn-klEITFKIRKgMKWSDGRPITADDWIMTWRIHTDKavgsnsyds------ffidgkpiv 149 Thermus thermop...
YP_001471151  79 vtNEIRPA--LAKSWTVsed-grEVTFKIRE-AYWSDGTAITSDDVIFTFEYFVMNsyargnsvarftipdekgenkpii 154 Thermotoga lett...
ZP_04034137   75 ktYQIEPA--LAASWTItge-skVYTFKLRKgVKWSDGRDLTADDVVFTYTQIVANpeakggda---------gnfagvk 142 Meiothermus sil...
ZP_04040253   73 --YTQAPEgnLAKSWEVrnn-glTVIFRLREgARWSDGQAIDADDVIFSATVHADQrvnsnarss------fildgqpir 143 Meiothermus rub...
ZP_04034134   90 -lTFELGGv-LAESWSFsrd-arTVTVKLRKgVKWSDGVPFTADDVIFTFTEVAANpnlrgnqaat-----ltvagtplk 161 Meiothermus sil...
YP_002787786  80 atYKIEPA--LAESWTIspd-grTYTFKLRQgVKWSDGQAFDADDVVFTYKNIIMNpearagdvgn-----frldgknve 151 Deinococcus des...
YP_604808    121 ytYEYVPA--AAESYTIspd-krTYTFTLRPeLKWSDGQAITADDYISTFEIYSKDedanlnayl-------fdngkpvt 190 Deinococcus geo...
Q9RU24        78 vtGNYAPY--MAEKYTQsad-krTFTFDIRKgMKWSDGKPITVDDWITAYTIDSNKdvgsntfdy------wtinnqpik 148 Deinococcus rad...
YP_002785758  79 rnDEFIPY--MADGKPVvsnnnkRFVVKIRQgMKFSDGQAITADDWVSTMTIHKDDkvgsnsfds------fflnkkpit 150 Deinococcus des...
YP_001738549 189 LEIVD--DYTFRMIfk--ePNMVLPWRITkswvagtsfvvpshyikqfhpkyvgeekaqqiakengfdnwwqfvqarcln 264 Thermotoga sp. RQ2
YP_143735    150 LRKLD--DYTIRFIypktdAEAFAIASFApwpahvfgpvyqke-----------------------------gaegikkm 198 Thermus thermop...
YP_001471151 155 WQKID--DKTVKAIlp--sSYGPFFTVLShvyiypkhkleplidk--------------------------ndlgsvnkl 204 Thermotoga lett...
ZP_04034137  143 IEKVD--AGTVRFTlp--kPAPAFIHYMRlpimpkhkllpfsqeg-------------------------gkkpgdinna 193 Meiothermus sil...
ZP_04040253  144 WTKVD--QYTVRADfp--kPYAPALIQGWyiapehifgpayra-----------------------------gvqqlqal 190 Meiothermus rub...
ZP_04034134  162 FEKVD--DLTFRVTsi--kPYGAVLQALTfspilprhklaqfnpl--------------------------qdpqgfsra 211 Meiothermus sil...
YP_002787786 152 IAKVD--ASTVRFTlp--rAAPAFLLQQRyfimprhkllkfsqeg-------------------------gakaadinga 202 Deinococcus des...
YP_604808    191 WKKLGdlKFSVTFPra-tvQNTETVSYFTplpdhifgatyrkaggg------------------------aagikavral 245 Deinococcus geo...
Q9RU24       149 VTKVDsnTLKVVFPka-dvTAIEFLSGIFlpqpthvfmpvwkak----------------------------gaqgikdm 199 Deinococcus rad...
YP_002785758 151 IKKID--TYTLQFDfp--qPSSQAYSRMAftpwpdhvfgktyra---------------------------ggaeaikkm 199 Deinococcus des...
YP_001738549 265 sdswlrNPDLPVLFPWKLSRRTTdTMLVLERNPYYFkid--peGNQLPYIDEIVHYLVqnsqmlvFKAITG---EIDMQG 339 Thermotoga sp. RQ2
YP_143735    199 wtlnedPAKIVSAGPWVVESYRPgERVVLKRNPSFGewnkdeaGNPLPYLDRYEIRIVkdvnaalAEFLAG---NIDIFN 275 Thermus thermop...
YP_001471151 205 wlsntdPKEIVVNGPYKLSQVITdQKIVLERNPYYWkvd--rfGNRLPYFDRVEYLIVrdaevrlAKFMAG---EIDFMA 279 Thermotoga lett...
ZP_04034137  194 wptnvdPDEVVGTGPFKLQSYTPgQKVTLVKNPNYWkrd--adGTPLPYLDRLEFLIIpdsqaqvAQFLAGnlgQLNITG 271 Meiothermus sil...
ZP_04040253  191 wnldtpPAQVVSGGPFKLDSYVKgERVVLVRNPNYWgvd--drNNPVAYLERYTVQVVpdlnaqlARFLAG---EADTFA 265 Meiothermus rub...
ZP_04034134  212 wstntdPKEIVGTGPFVIQNYTVdQKVALVRNPYSWrrd--pqGNPLPYFDRLEYLIIrdpnlqvAQFQAG---NLDQVP 286 Meiothermus sil...
YP_002787786 203 wptnvnETEVVGTGPFKLATYTAgQKVTLTRNPNYWkvd--aaGKKLPYLDRLEFLVIrdpqaqvAQFLAG---NLDQLN 277 Deinococcus des...
YP_604808    246 wdlntdPSKIVSAGPFKVGSYKRgERLNLVKNPYYGqwnkdsqGRPLPYLDGLQYNIVpdqnaalAQFLAG---NTDLFS 322 Deinococcus geo...
Q9RU24       200 wtistnPDNIVTSGPFMLDRYVRgERAILKKNPYFGewnkdsaGKSLPYLDGIQINIVadanaqlAQFLAG---NLDTYS 276 Deinococcus rad...
YP_002785758 200 wtlgtnPSEIVSPGAWVLESLRAgERAVLKKNPHWGdwnqdsrGNELPYLDRTSYRIVgdanaalAAYLSG---QIDTVA 276 Deinococcus des...
YP_001738549 340 rnlsvadlqlllanqekggyRVIFE------RQAIg--sDVTLWFNqnyeedeilasiLRDVRFRQAISLAINREEIWQL 411 Thermotoga sp. RQ2
YP_143735    276 pstvdqisqi-rqavqqgrlDATIKv----nASPVa--sSQFMVFNwnkasdpfkqslFRSDKFRRAMSHLVNRQAVIDI 348 Thermus thermop...
YP_001471151 280 isskdypml--kqqeltgkaPYKVYatqpnqATPS----PIHISFNfdvddp-qlrelFRTLEFREAMEYALNRERIIDE 352 Thermotoga lett...
ZP_04034137  272 tdfptlk------qrevqgaPIKVVqf--raLFGS----PPHLAFNyddknp-elaalFRKTEFRRAIQSAVNRKRIIDD 338 Meiothermus sil...
ZP_04040253  266 aanadqvaqv-lerirgnrlRAEIF------PNADvtlgTNFIVFNwnhkdp-fkeslFRQVKFRRAMAHLMDKKSMIEV 337 Meiothermus rub...
ZP_04034134  287 itgaqypdl---krqevagaKIRVL------KGTTiytsPPHWGFNfdaknp-elaelFRDLTFRKAMQAALNRTRIIED 356 Meiothermus sil...
YP_002787786 278 itgaqfpdl---kqkevagaPFKVM------RSTAlfgsPPFVAYNfdakdp-alakvFSDVRFRRAMQGAVNRERIIET 347 Deinococcus des...
YP_604808    323 psnrdqlaqv-vaaknsgklKVDVLa----nAGPNa--sVDFLYFNwnkasdpfkqqlFRNTKFRQAMSMLVNKDAMIDQ 395 Deinococcus geo...
Q9RU24       277 pdnrdkla-----qvksamdGGKVKgtlipnASARa--sSDFMVFNmddsat-fktklFSNVKFRQAMSMLMNRDAMVDL 348 Deinococcus rad...
YP_002785758 277 vrnaddlaq---ikkamdagSLKAFlr--pnVSPQa--tSQWIVFNwnkasdpakqklFRDVRFRRAMSHLANRQAMVQL 349 Deinococcus des...
YP_001738549 412 VYhGLGEPrqaslikgvky-ydpewekayaEYDPERANKLLDEMGLtkRDSEGYRLRPDGkrlEITIEYPtgvftawDDA 490 Thermotoga sp. RQ2
YP_143735    349 VYgGLGIPmyssvypvlt--qwinpkvpkyEYDPKQAAKLLAELGFtkKDREGYLVDSKGrriEFNLATNagn-tqrEQI 425 Thermus thermop...
YP_001471151 353 VFaGLAIPdaglmlpsnkafynpkieellrPYDLKKANELLDKIGLnkKDKDGYRLFSNGkrvEFNLLVQssp-qeyQDV 431 Thermotoga lett...
ZP_04034137  339 VYnGLAELpgngvapvse--wyydttkllgTYDLAAANAALDKLGLk-KGADGIRLLPSGkplEFTLTYGsns-stfTAI 414 Meiothermus sil...
ZP_04040253  338 ALgGLGQPqwspisipnk--afftddvvkyEFSPQKAAQLLAELGFrsKNRDGWLVNAQGkvlEFNLVTNqgn-nvrERI 414 Meiothermus rub...
ZP_04034134  357 VYnGLASLpghgvapgtf--wyydtraylgKYDLQKAAGLLESLGLk-RGPDGLRRLPSGkplEFTLTYAsds-ipiSAI 432 Meiothermus sil...
YP_002787786 348 VYnGLASLpghgvapanka-fytnttkqlgSFNLSAVNEALDAIGLsrKNAAGIRLLPNGrplEFDLTYGtds-svyPPI 425 Deinococcus des...
YP_604808    396 VMgGLAVPawtsvyplys--ewvapnvdkyKYNPAAANKLLDELGFkkRGADGIRVDSKGnrlSFTLLTNsen-nrrQQL 472 Deinococcus geo...
Q9RU24       349 ALgGLGEPtytsvypvyk--dwipsgmdkyKFNPTAAAKLLAELGFtkKGSDGILVDKAGnklEFTLITNaen-nrrQSY 425 Deinococcus rad...
YP_002785758 350 ALgGLGTEtyfsvypifkqqmaaganapkyPFNPGEATRLLAQMGYtkKNAQGFLVDKAGkvlEFNLSTNagn-tvrEQL 428 Deinococcus des...
YP_001738549 491 LQMIKNYVEKIGVKVLLKs-eERSLWDTRNQTgq--------iQIAAWWFdrns-----dvfgDPSLLLgyrtwaplsyi 556 Thermotoga sp. RQ2
YP_143735    426 AKLIVDEAKKVGVKVNFQa-iDFNTLVGQLLSsgpd----rpfDAIIIGLtgggldwpfgsnvVPCKGNlhmwnk----- 495 Thermus thermop...
YP_001471151 432 AVIFAQDLEKIGIKVNLQi-lDSSLVGQMFGAgn--------fQAGVRAFgn---------qpDPQLRKaiwqpgtqlyy 493 Thermotoga lett...
ZP_04034137  415 ATIIQNDLKAIGVKANLQgvlAANLLSTGRGKd---------wDAIILGFgd---------qpDPELRTpiwkpggdlyy 476 Meiothermus sil...
ZP_04040253  415 AQIFRDEARKIGVKVEYRp-iDFNELVRQLTSpaadg--trdfDAILIGLtg---------giEPAFSRnvwelngplhm 482 Meiothermus rub...
ZP_04034134  433 ATILQNDLRQIGVKLNLQg-iQQSTVLSTATSgn--------fESIIVAFgd---------qpDPQLRKdiwqpggqlny 494 Meiothermus sil...
YP_002787786 426 ATILQSDFAKVGVKVNLKgilSSRLLSTGQSGd---------wEMILHAFgd---------qpDPELRRpiwqpggslyy 487 Deinococcus des...
YP_604808    473 ARLFADEAKKAGVEVKTNf-iPFNQLLDIAYPesdaakldrkfDAAITGLggg-------gfiNPVGVAslltcggdln- 543 Deinococcus geo...
Q9RU24       426 AKVIQDEAKKVGVKINVSa-iAFNQMTTLLDAkdnfg--rrnfDAIIIGLtgggq---vypvsGPSVVEckglgdggnlh 499 Deinococcus rad...
YP_002785758 429 GRIFADEAKKVGVKVNFTp-iDFNNLVNQLTAkgen----rpfDAILLGLsggsniwsfgsnvVPCGTNlhsynnp---- 499 Deinococcus des...
YP_001738549 557 wy------nqgrqggkapeegTDMWKIYELYDLArkepDDQKRDEYMRQLLEIHKKnLWAIGTVGAlpqPVVVKN-NFEN 629 Thermotoga sp. RQ2
YP_143735    496 ---------------sgqcldPRETLMEKLYYQGrtelDFKKRVEIGYRMQEVEAElLPVIYIAGPn-yHPAWNN-RLGG 558 Thermus thermop...
YP_001471151 494 whystmdktktppqpvfenmfDWEKRIWELFEKGqvemDPAKRKVYYDEWQELYHVyLPVIFVCKGm-nIWGINN-TLGN 571 Thermotoga lett...
ZP_04034137  477 whqst-qpttpggqpqfsnflPWEKEIYDLWEKAasttNFTQRKALYDRWQAIFAReAMVIMIAKAn-aVGAVST-KYGN 553 Meiothermus sil...
ZP_04040253  483 wn-------lgiggknpakveAFEVLIDTLMKRGattlDQAQRRQIYVQFQKVVAEnLPIIYTVAPa--YNPARLtRLGG 553 Meiothermus rub...
ZP_04034134  495 whrsv-wpdkgeqdpkfdqmfGWEKNIWEIFRQAeqlgDQTERKRLYDRWQLLFAQnLPVIMIVKPd--AVAAGStRLGN 571 Meiothermus sil...
YP_002787786 488 whrst-qpakdgdpaivsrmaKWERDIYNIFNDAatttSASQRKALYTRWQLIFAQnLPVTPIAKPe-nIGAISN-KYGN 564 Deinococcus des...
YP_604808    544 -----------gynqskkciqPWETQQANLFFKStaefDQAKRKAIANQIQQLQANnLGYIYLLSPn-aHYAWDQ-RVQG 610 Deinococcus geo...
Q9RU24       500 -----------mfnqsnkcrfPFETQAVNLFWKGraefDLAKRKAIAAQIQRNEMEnQPYIQLAAQt-vHFAWTD-RVQG 566 Deinococcus rad...
YP_002785758 500 --------------tngacatSQEQLMTKLYYQGdaefDDAKRRAIGGRIMQAEGElQPVIYLVGGn--YHATWNeRVGG 563 Deinococcus des...
YP_001738549 630 V 630 Thermotoga sp. RQ2
YP_143735    559 E 559 Thermus thermophilus HB8
YP_001471151 572 A 572 Thermotoga lettingae TMO
ZP_04034137  554 Y 554 Meiothermus silvanus DSM 9946
ZP_04040253  554 M 554 Meiothermus ruber DSM 1279
ZP_04034134  572 F 572 Meiothermus silvanus DSM 9946
YP_002787786 565 Y 565 Deinococcus deserti VCD115
YP_604808    611 E 611 Deinococcus geothermalis DSM 11300
Q9RU24       567 E 567 Deinococcus radiodurans R1
YP_002785758 564 E 564 Deinococcus deserti VCD115
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