Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_6

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cd08494: PBP2_NikA_DppA_OppA_like_6 
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: 173859
View PSSM: cd08494
Aligned: 27 rows
Threshold Bit Score: 514.871
Threshold Setting Gi: 229817096
Created: 5-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_356217    42 ALTLGMtveptgLDPTIaapVAIGQVTWqNIFEGLVTIDskGKVKPQLAESWEISpDGKSYTFKLRKgVTFHDGEAFDSA 121 Agrobacterium tu...
ZP_03388296  31 VLTIGAtaapptLDLVSnaaAAIPQVLLyNVYETLVRVDdsGKLVGLLAKSWKLSdDGLRLTFRLDPnARFASGAWVTSA 110 Propionibacteriu...
YP_715023    44 TVTIGAvleptsLDITRtsgVAVGQILLgNVYEGLVKRDqkGVVSPALATSYTISpDGLTYTFTLAGnAAFQDGAPVRAA 123 Frankia alni ACN14a
AAP21660     51 TVDVRLvleptsLDIAStagAALDQILLdNIYQGLLTRDenNKIEPSLATSYDTSpDGLTYTFRLAKsATFHDGTKVTAA 130 Streptomyces hyg...
NP_696330    73 TVTIGLklaptnLDIRNtagSALDQILIgNVYEGIVARDskNQVAPAIASSWETSkDGLTYTFHLNKnMTFFNGDKLDAE 152 Bifidobacterium ...
ZP_03936866  55 VLKIGLrtapasLDIRTddsDSLQQALIeNVYETLIKRDgnNALKPGLAQSWSVSsDGLNYRFRIRSgVKFANGDVMDSG 134 Gardnerella vagi...
NP_695594    27 DVTIGIddmpqsLDIRSdssAAAERLLVdNVYETLVTVDqdNKLQPGLATSWKTSdDGLTVTLTLQSgVTFSNGHTLDAS 106 Bifidobacterium ...
ZP_04447378  55 TLAVGVtdvpdtLDIRTvnnASLDRVLIgNVYETLLGRNsdNGITAGLASSWKTSdDGLTLTFTLRSgLRFANGHTLDAA 134 Bifidobacterium ...
ZP_02917870  56 TVSIGLrdapesLDIRTqqgHAVEQALLgNVYETLVSRSetNKLQPGLASSWQISdDGLTYTFTLRSgVKFSNGHSLDSA 135 Bifidobacterium ...
ZP_02964118  55 KLEVGLldeptsLDIRSnseRSVQQALMgNVYETLVTFNdeQAIASGLAARWTQTtDGLRYTFFLRNgLTFSDGTPLDAS 134 Bifidobacterium ...
NP_356217   122 VAKFSLDRARGeasvnpqkrffaaidsIETPDADTLVLKLkqpagSLIYWlgwpasvmva-pksaeanrttPVGTGPFKF 200 Agrobacterium tu...
ZP_03388296 111 AVKASLERMRGgsaspvnqanlaaikaIHTPDDSTVILDLsnrdnFLLFNlastsgvvid--patkdlatrPKGSGPYVV 188 Propionibacteriu...
YP_715023   124 DVVSSLTKVIGpnstnphasdlaslsaVTSPDPRTVVLTLkerdsGLLFNltgpagvvvr--egatgldghPDGTGPFRF 201 Frankia alni ACN14a
AAP21660    131 DAVWSLQQATAkgsknpdaaalasvksVSASDDHTVVVTLkhrdtGFTWGltgragvvfkkgtdfsslagnENGTGPFKL 210 Streptomyces hyg...
NP_696330   153 DVAWSINELIAkgyhdad--alaavskVEAKDADTAVITLktpnsNLLWTltgraglvfd-kdakydlktqAVGSGPYTV 229 Bifidobacterium ...
ZP_03936866 135 SVLQSLQQGITksypgye--kltnitsVSNSGPDILNISLkmpdpLLLRRlagragivyd-traslnyasdAMGTGPFKV 211 Gardnerella vagi...
NP_695594   107 DAVWSLQQNVTnkvadvd--elgdlasVANPNATTVVITLakpnpTLLRAlsgrlgivydsesssadyqrkAIGSGPFTV 184 Bifidobacterium ...
ZP_04447378 135 SVVWSLQQAVSnkwpgadt-klaalasVTNPNATTVVITLkqpdaTLPRTlsgrlgivyd-saanidytnqAMGSGPYRI 212 Bifidobacterium ...
ZP_02917870 136 DAVWSLQNAVNnhyvdad--qldglqqVDNPDAHTLVITLskpnpRLLRAlsgragivyd-eesdndyaktAVGSGPFTV 212 Bifidobacterium ...
ZP_02964118 135 SVVRSLQQTLAgdhtndg---lsnitaVENNDARSVTFTLsspnpRLLPAlasqagaivnpnaknpdfahhSYGSGPFIV 211 Bifidobacterium ...
NP_356217   201 VSWAKgDKVELEKNAAYWDkavAVKLDKATFRFvadpqaqaaALKSGdiDAFPefgapelmtsfdgDKRLGTFVGNTElK 280 Agrobacterium tu...
ZP_03388296 189 TEFTPgHSVTLSPSPQPWH---EGNRPTVRFAYysdptsqtaALLSGdlDVVSdmttpqalsrftgNPNYRVLRGTTNgE 265 Propionibacteriu...
YP_715023   202 DSWRRgDSITLVRNDAYRGp--KAKVARVVFRYltdanaqnnAVRTGqvDVGVisdndl-ieayrgNPKFTIAEGTTTdK 278 Frankia alni ACN14a
AAP21660    211 SGWKRgSSITFVRNDAYWGq--KAKVAKVVFHYikddnaagnAQQTGqtDIETaadatl-lqpfsdKSEYTVLRGDTTdK 287 Streptomyces hyg...
NP_696330   230 AKFVEnSSITLKANEKYWGk-nKAKTPTVVVKYladdnaavnALKSGdvQVLApitenlaepfksdSAKYTVKAGNGTdK 308 Bifidobacterium ...
ZP_03936866 212 NGYSKgSDLVLVRNDKYWGt--ASGCASITLKYfnddtslanAMQNGdiQMAVpldgne-nkrmasMPNTQLVEGQSTrI 288 Gardnerella vagi...
NP_695594   185 ADFQPgHSLKLARSDTYHGt--KAASNVVEFMQysdadalskALTDGslDMAApvsast-atglngKDGLTVKEGATTdK 261 Bifidobacterium ...
ZP_04447378 213 TNFTPsQRIAFAAVSGSTAk--THTVTVRNYSSnsn---llkAARSGdvDLAIpsdpas-adsladDQNLRVSAGTSEnK 286 Bifidobacterium ...
ZP_02917870 213 ARASK-SEIVLQRNDSYWGt--KAASSQITLYYyssessltsAMEGGkiSMALplsada-aetlnaTRGISADSGISFdK 288 Bifidobacterium ...
ZP_02964118 212 NAVQP-GSIELTRNEHYWAd--KPKTSQATLRYytdeqkmadDLKAGklNVALprsahi-aeqlshTSGITLQDGFSTrK 287 Bifidobacterium ...
NP_356217   281 VVAGMNnark-pfnDKRVRQALMMAVDRGTVIEGAWsGYGTAiGSHYTPndrgYVDTTgvhSFDIDKAKALLAEAGYadg 359 Agrobacterium tu...
ZP_03388296 266 VVLGMNntsk-alsDRRVRQAILMAIDRKGLLDVVWnGQGTLiGSMVPPtdpwYTDLShtwPHDPARARKLLADAGYgng 344 Propionibacteriu...
YP_715023   279 FTLAFNqdrg-plaDARVRHAIRQGIDKDGLIKVLG-AGTRI-GSPVPPldpwYSDLTsidRYDPASARRLLAQAGHggg 355 Frankia alni ACN14a
AAP21660    288 FTLAFNnasg-ptkDVRVRRAIRRAIDNAGLIKALG-GAAKPvGGPVPAtdpgYEDLTaidAYDPAGAKKLLRQAGYrgg 365 Streptomyces hyg...
NP_696330   309 FVLGFNnasgsklaDKRIRQAIRYAINHKELIASRG-GADKAlGGPIPSldpgYEDLTnlyPYDQNKAKSLMAEAGYstd 387 Bifidobacterium ...
ZP_03936866 289 RMIAYNtgissifcDQHVRRASSYAMDINTVLSADP-FGGQIvRGPISPlspgYEDLSgtyPHDPQKARSLFSYFSAayl 367 Gardnerella vagi...
NP_695594   262 VLLAYNngtdsllsDEQARKAFRYQIDAAGIASAQPdAAGAL-GGPISLlepgYEDLTglyPHDENQAGQMFSYFGAqyl 340 Bifidobacterium ...
ZP_04447378 287 VTLLYNndadsifsDVQARTALRMMLDKTALLKDRS-DVAQPlGGPIGPlepgYEDLTgliAHNADRGRQLMSYFSSsyi 365 Bifidobacterium ...
ZP_02917870 289 VMLAFNnanesilvDQQMRKVMRYAIDARSIAKTANdSYGAL-GGPISPledgYEDLTelfPHDLTQAQQLRSYFGTgyi 367 Bifidobacterium ...
ZP_02964118 288 TLLALNsksespfsDEQVRQFTRYAIDARQIANAEPgAKAQL-SGPISQmqpgYVDLDnlfQHDLGKASSMRWYFAAdyf 366 Bifidobacterium ...
NP_356217   360 fSFTIKAPqma-yaQRTSQILQAMLAE-IGVTMTIEttefPAKWVADVLKgadYDMTIVAHAEpmDIDIYARDPYYFnYK 437 Agrobacterium tu...
ZP_03388296 345 lTLRLRTAalp-yaTAASRVVASELAQ-VGINVVTDelefPARWLDVVYThadYDLTIVAHVEarDIVNWANPDYYWrYH 422 Propionibacteriu...
YP_715023   356 lRLGLTVPni--ypPSIGDYVTSQLRE-IGVTVDLHrv-eFPAWLTGVYTkhdYDLSIVDHAEarDLAFYVKPGYYFgDR 431 Frankia alni ACN14a
AAP21660    366 lKLTLQIPni--ypAEIGDYLASELKR-VGIQLTVRpv-eFQTWLDSVYTkhdYQLSLVDHAEarDLNNFANPAYYFgYD 441 Streptomyces hyg...
NP_696330   388 kPLQLTLTyaniygTELGDQLRSQLKP-IGIDLKVNvv-eFSTWLQDVYTnhtFDISLVDHNEshDFASWTDPTYYFgYD 465 Bifidobacterium ...
ZP_03936866 368 gKITFLVPlg---mSNIGNALASQLNAtGGFRVNVEev-dENTMKQRIHDg-kYDLALTWMNHtlDSGAYADTKSTYlFQ 442 Gardnerella vagi...
NP_695594   341 tTVNLVVPee---yRSLAETIKQQIERqPRPTVNLEvl-sDEDYAKRIKDg-kWELTVMSMDGtdDAGIFADPDSMFhYD 415 Bifidobacterium ...
ZP_04447378 366 dTINLVTSet---yEPLAQNIAHQLQE-QGISVEVSa--lSDAGVQDCLSkrnFQLLLTTINGvdGTADFADPNGPSrYT 439 Bifidobacterium ...
ZP_02917870 368 gTIDLLIPqq---yETIGNTVKEQIEQ-LGVSVNMEvl-dTATVQQRVNDg-sYTIALITMSGenDASVFTDGQSVFhFE 441 Bifidobacterium ...
ZP_02964118 367 kPFNLLADea---hRELAQTLVDQIAA-IPMPVSLEvv-dSATLNSRVQSg-dYTCALIEMDDphDYTRFVDGSAMFgYV 440 Bifidobacterium ...
NP_356217   438 NPAFNEVIANVektaNAGEQEALYGDAQKILAE-DVPALFLFVMpkLGVWDRKVKGL 493 Agrobacterium tumefaciens str. C58
ZP_03388296 423 NKEFNRLIESArt-gPADRTNETMMQASRILAT-DAAGGFLFLMpkITISKSGITGL 477 Propionibacterium acnes SK137
YP_715023   432 SPQARDLAKAGataaSDAERDTALRGLARRYSE-DAIADWLLLAkaRQVARVGVTGY 487 Frankia alni ACN14a
AAP21660    442 NANVQKWYAAArtasSDAERDALLKKAARQVSE-DAAADWLFVNqtLTVVHSGVTGV 497 Streptomyces hygroscopicus subsp. yingc...
NP_696330   466 NKNVTKLYNEGvaatSDKERDAKFAAAAKLVSE-DAPADWLFNYriTTATAKGVEGF 521 Bifidobacterium longum NCC2705
ZP_03936866 443 DHESQKYFAQAmkstNAEGYESNIKQYARELNN-YAVSDWMYARksIVVAKSNVSGY 498 Gardnerella vaginalis ATCC 14019
NP_695594   416 HTEAQQAYADAra-aTNDADYEARMKAYARLISeDAASDWLYTRkcFTVASTKVSGY 471 Bifidobacterium longum NCC2705
ZP_04447378 440 NADAQAQYTQAvhatTQEAYENGLKAYARTVSS-TAASDWLYARktAVIASTQLAGY 495 Bifidobacterium angulatum DSM 20098
ZP_02917870 442 NGDCQRAYADAlaatNDDDYQERMRTYARTVSE-NAACDWLYTRknFMAVSDRLQGY 497 Bifidobacterium dentium ATCC 27678
ZP_02964118 441 NGTVQQQYRKAleqtDFKDYREQLREFDRLVSD-DAASAWLYTGkdYVAAQNDVQGV 496 Bifidobacterium animalis subsp. lactis ...
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