Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_8

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cd08495: PBP2_NikA_DppA_OppA_like_8 
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: 173860
View PSSM: cd08495
Aligned: 19 rows
Threshold Bit Score: 463.348
Threshold Setting Gi: 163744609
Created: 8-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_002498493  28 VLRIGMtasDIPLTTGQADn---GGEGMRFTgy---taYDALINWDlgsa----dkaAVLTPGLATAWKVDpnd-trKWI 96  Methylobacteriu...
YP_001821869  46 TLIIGA---EGEIPTLDPH----RASGTPVLrvi-dalFDPLIREDlgte---taqaPELRPALAESWQASpd--arTYT 112 Streptomyces gr...
ZP_03588251    6 ILRVAL---DWAVDEIDPPrsfgGWNTGRVVqq----tHESLVEDDfdtaptpagvpTQIVPRLAEHVDMSqd--arRFV 76  Burkholderia mu...
YP_885480     35 VFVIAI---ESEADILDPQva-gGWVSWRINrq----iFEPLVDEDlsmps-seatvPPLRPGLAESWDISdd--glEYT 103 Mycobacterium s...
ZP_01441843   34 RLRIAMtlsDIPTTTGMPSq---GGEGMRFAgy---pvFEPLVAWNlred---tdrrAETMPGLAKSWEIDped-ntRWI 103 Roseovarius sp....
YP_675190     30 TFRAVI---SLPIQTLDPQk---SIAGLAGDalr--tvFQTLTFVQs---------dGSVAPMLAQSWEIDpnseglQWI 92  Mesorhizobium s...
YP_386867     50 TVTVAM---FQRIASLDPAhs-sLYEPHSIAan----vFETLVTVSr---------nGTVQPAVAESWNVTpd--grRWT 110 Desulfovibrio d...
ZP_02151969    4 IAQARL---GLHDPHDCTD----ATDELTVLha----vYDTLVKREg----------QGFVPALARSWEVSed--akVWT 60  Oceanibulbus in...
YP_002784321  47 TLKMAW---TLAPNNLDPH----QSSNYQVDfsylapvYDRLTQAVs---------gPAIEPMLAESWQFSpd--glSAD 108 Rhodococcus opa...
YP_002784322  44 TLRVAG---NVVPNNLDPH----QSGNYQIDfpflspvYDRLTQAVs---------gPTIAPMVAESWTFAdd--grSVD 105 Rhodococcus opa...
YP_002498493  97 FTLREgVTFHDGSPFNADAVVWNLDKILKtdspqfdprqsaqgrtripgvasYRAIDPKTVEIATktpdaTFPYQIswil 176 Methylobacteriu...
YP_001821869 113 LKLREgVEFADGSPFDAAAVKANFDRIMDessafhdptaagnmkfltrwikeVDVRDPRTVVLGLtepyaGLPRVLtdrr 192 Streptomyces gr...
ZP_03588251   77 FRLRDgVRFHDGTPLDAEAVVLNYERMCCpespyysaviadfnragielvedVRALDARTVAFTLsqpfpDFLRYMtqed 156 Burkholderia mu...
YP_885480    104 FHIRKdVKFHDGTPLDARAVEYNVRRMWDksspmynaraagqtgfvwkfldsVQTVDDHTLKMRLsqpfsEFLRMLaqgg 183 Mycobacterium s...
ZP_01441843  104 FNLRPdVAFHDGTLWNADAAIWNLERFWDedspqfevaaagtaqgrvsqmssWEKIDDMTIALITtapssYFPQALtqll 183 Roseovarius sp....
YP_675190     93 VKLKPdVVFHDGEPFNAAAVAANWKRLLDpkvpiqar-------sninmiteVEAIDDLTVRFTTnrpfsGFPMAIghav 165 Mesorhizobium s...
YP_386867    111 FTLHEgRSFHDGSPLNAYAVEYSFQRLMDpahpqytpypd-wkrllfgqvnsIRALDDNTLEIELdnpyaPLLHNLatpg 189 Desulfovibrio d...
ZP_02151969   61 FSLEPdVQFHDGTPCDAAAVAASLERMARedkgytlgapa--vwrqflgeakLEVLDPTRLRVTLtapmaDLLDVLeqgf 138 Oceanibulbus in...
YP_002784321 109 FVLRTdAKFHDGTPVDAAAVVKSLDRARDpqrarsag--------slavitsVQAVNDNTVRITTsrpaaDLPAILsttt 180 Rhodococcus opa...
YP_002784322 106 FTLRNdVTFHDGTPVDAQAVVASLARARDpqkskvag--------rfdmvtgVDAVDGNRVRISTsrpalDLPAVLstte 177 Rhodococcus opa...
YP_002498493 177 msspanwe----kqgrswdavaksPSGTGPWKITAFVPr---ERAELTPNKDYWDkarVPKLDKLVLIPlpeanaRVAAL 249 Methylobacteriu...
YP_001821869 193 msiispaa----lrthrpddiglhPVGTGPFTQQSADRg---KRITLKRNTAYWGg--SPKTPSIIVESvtdpttLAIAA 263 Streptomyces gr...
ZP_03588251  157 apgaqslisptairelgpdgcadrAPGTGAFRFHRRFDtpggSAVELLRNEHYWAg--PPSIDGIQFLPypdqeeRVRAL 234 Burkholderia mu...
YP_885480    184 ngstaimsp--talqtygedvadhPVGTGPFKFKERIRg---ERIDLVRNDDYWGk--VPYIDGVVFRPlpdpsaRTAAL 256 Mycobacterium s...
ZP_01441843  184 faspskfe----ekggdwgqvgqdPAGTGPFRITNVVPr---QSITMQKNPDYWDparMAQVDEIVLTPipdantRLAAL 256 Roseovarius sp....
YP_675190    166 ssivspks----iaagllddpnasPAGTGPYRIARFTLp---DELEVEKFDNYWGk--TGNAEKLVFISrpdeqaRMAAF 236 Mesorhizobium s...
YP_386867    190 asivsprs-----lqemhdgrtaiPAGSGPFRVASYSP----EAVTLIPAAGHTPp--PRCNVRYEYYAss--ssALEAL 256 Desulfovibrio d...
ZP_02151969  139 ivapsgl-------aaldtgdhsaQIGSGPYRITQISP----ERISATRVAGHFSg--TPANAEITWLLepdaarRQAML 205 Oceanibulbus in...
YP_002784321 181 aaivnpv------aidggvdlsveTAGSGPYVAEQIRRg---DRIIYKRFDGYWDp-eAQKAANLEIIGisddnaRLNAF 250 Rhodococcus opa...
YP_002784322 178 aaivnvk------aldagldigrtDAGSGPYRFDQVRPg---DRVTYVRYDGYWDp-dAQKPQRLELIGmaddnsRLNAF 247 Rhodococcus opa...
YP_002498493 250 RSGqvDWIEapapdal---aslkaaGFRLVTNLYp-hNWTWHLSrvegspwnDIRVRKAANLAVDREGLKEFLG-GLAVP 324 Methylobacteriu...
YP_001821869 264 QTGevDAILsagaqqv---qqladgGTMTAQYPEpanQYFIRLNtkia-ptdDAVFRRALNHAVDRRAIATLTG-RQVAP 338 Streptomyces gr...
ZP_03588251  235 TQGrvDIAYslegsdl---aelasrGFTVPEFSPp-yLWYLIFNlrdp-nmaDVRVRQAIAHAVDRQALCDELFpGAAAP 309 Burkholderia mu...
YP_885480    257 RSGdvDMIAvpnpdsi---dnlvseGYQLSEGTPp-hTWYLSFNmkdr-ytsIPEVRQAINLAVDREGMAKDMLrGSVTP 331 Mycobacterium s...
ZP_01441843  257 RSGqvDWIEvpppdaip-gleaagfEISMKTYPHi-wPHIFSFNegs--pflDKRVRQAANYAIDREGLAYLMN-GTVRP 331 Roseovarius sp....
YP_675190    237 LAGeaDANFyvgaesr--grvegsqDLRTEAIASi-rEFIVHLPmkvd-alqDIRVRRALNHAIDRDQIVKSVFgGVAEP 312 Mesorhizobium s...
YP_386867    257 LSGraDIVPglteqde--ktaqrlgAYTIIRHPQl-sVIFLACNgase-kmrSPEIRRAVSLSINRNSLATVVLgANGMP 332 Desulfovibrio d...
ZP_02151969  206 AEGavQVANgldfg------asralGTMRHEFLSp-vAIIYLLNaarg-plaDARVRRALSLAVDREALVETVMqGAARP 277 Oceanibulbus in...
YP_002784321 251 RSGqiDVMLakagqtdelqtllrqpQYQMHTFPVs-qYYAVQLDigqq-gltDPRVRQALNYAIDRDSINSALLkDQCQP 328 Rhodococcus opa...
YP_002784322 248 RSGqvDAIKvdpdqydeiravtggsGFEVHEYPTv-qSYAVQLDigtp-gleNAKVRQALNYAIDREGINSALLnGKCAP 325 Rhodococcus opa...
YP_002498493 325 AeGFMTPGHPWFGkpsf--tvkYDPEAAKKLLKEAGYgpdk--------pittKILISASgsgqmqpLPMNEFIQQNLAE 394 Methylobacteriu...
YP_001821869 339 StGPLPRGNEAYRegseaaaysYDPEEARRLIRESGVstp----------vtlRMLAPDSgpgfsqaTEIMSLIQQDLKA 408 Streptomyces gr...
ZP_03588251  310 AvSAIPPGAPAHDpnacterypYDPDRARKLLAEAGMahg----------mtlEVEGAQAgsaqlnsGSIYKRLAHDLDQ 379 Burkholderia mu...
YP_885480    332 AwGVQALSAGGYVerkd--iyqRNLDKARQLLASVGLadg----------fqtTLITSTDgsgqimpAQMAEFIQQNLAE 399 Mycobacterium s...
ZP_01441843  332 AsGYVPPEDAWYGsptq--dykYDPDRARELLAEAGYgpdn--------kvpmKVLTSSSgsgqllpVQMNQLMQQNLNE 401 Roseovarius sp....
YP_675190    313 AlSAIQPGVAGYEklp---iytYDVDKAAALLKEAGWtknangvlekdgkpfpTLVFMSGrgrvpndARLAQVTAAYLNQ 389 Mesorhizobium s...
YP_386867    333 AtGLLPPEMWAKDhslp--pyeYAPDKARQLLLRSGYpqgi---------sltALQLDASrpfmpspRLFAVTLKYLMAG 401 Desulfovibrio d...
ZP_02151969  278 LrGFVSPNHFGAGmgq---gaqMDRETARALLAEAGHgg------------gvTLEVDCPtrlpdeaERLTAALAAQLAE 342 Oceanibulbus in...
YP_002784321 329 IsQPIADGVNGHNsdvd-gkytYDPNKARQLLKEANApa------------dlKLRLITVsgl-spqQEMATAIQAQLAD 394 Rhodococcus opa...
YP_002784322 326 LsQPLPEGVDGHDdsrt-alytHDPVKAKALLKEAGApd------------nlSLRVIYVaga-spqQEMATSVQAQLRD 391 Rhodococcus opa...
YP_002498493 395 IGIKVDFEvv-eWNTLINIWRAga-ksDTARGAtgmnysyliqdpFTAFIRhaqcnlapp-ngtnwgfycDPEMDKLFDQ 471 Methylobacteriu...
YP_001821869 409 VGVRLDTQym-eFASLVAEEGNgy-ndTTHGSFngwttgadaadfLERMFSgelhppdg----vnrgwyrNRDVDGLFDR 482 Streptomyces gr...
ZP_03588251  380 VGIHLNVRlhpdWVAYCNQWRA-----GAPAGVafsems-wgmscDLWLAQilhgdnasp-hgfnvgynkDVILDDLLDR 452 Burkholderia mu...
YP_885480    400 IGIKVNIQtq-eWISYLGVWAR-----GMQDGVgmaqms-wgmtsPYWLYIvtsselqap-ngpnvgyysSPALDKAMNN 471 Mycobacterium s...
ZP_01441843  402 VGFACEIEvl-eWGQLINAFRAek-dsPAREGAdainms-lsfpgPAEWQRwfhgsnlpp-vgsnwgywqNEEFDALIDQ 477 Roseovarius sp....
YP_675190    390 IGIPTTLQid-eFATFYPAAMApd-grGTRFVHmswgfgqmdgaaFLCTVYgegrpq-------nfggyeNPKVGEACGK 460 Mesorhizobium s...
YP_386867    402 AGITLSIEt--lPPDALRERRAq----GDYDLFina------wvaDTADPDnlysthlyagpdnplhrvhIPELDRLIEE 469 Desulfovibrio d...
ZP_02151969  343 VDIALDVHthpeREDYAHMVRRk----EIRDLCvfd-------ssPMSTYRvlfekidsrvagswwqgyaNPQIEALIDE 411 Oceanibulbus in...
YP_002784321 395 VGVGLDIMpl-pAADAQTTMGEgsyslLNPRLTyptpaq-slqtnYLVPLRfpt--------------apSQEFTDAVNR 458 Rhodococcus opa...
YP_002784322 392 IGVDAQLLpi-pAVDAQSTFRQgdyelLNSRLAypipgq-slllnYMADYRfps--------------ppSAQFSETVLQ 455 Rhodococcus opa...
YP_002498493 472 VRSTf-DPAAQTAVLQKIHEKFVDDALFLMVTHDv-nPRAMSPKVKGF 517 Methylobacterium nodulans ORS 2060
YP_001821869 483 ARGEp-DPDRRTALYREAAESIAADAPWVFLYQDr-lPRLLSRKVEGV 528 Streptomyces griseus subsp. griseus NBRC 13350
ZP_03588251  453 ARVTl-APTDRAARYRAADARVMEMLPILPLFTSrrgMIAWSPRVTGL 499 Burkholderia multivorans CGD1
YP_885480    472 AIIAl-DPQEAEQWWRRANNIVSDEAALVPIVNDk-aPYVLAPYVSGF 517 Mycobacterium smegmatis str. MC2 155
ZP_01441843  478 VGVTf-DPEEVDALLARAHEVLVEEAPWLFVVHDm-nPRALAPNVEDF 523 Roseovarius sp. HTCC2601
YP_675190    461 IDNTf-DAAERARLIAEATKMVYEDAPAIFLVVPs-lLAGFNSTVKNL 506 Mesorhizobium sp. BNC1
YP_386867    470 SVSTp-VRGERARAYRRIQRIEREQMPCIPVMHSs-lPVILRRGISGM 515 Desulfovibrio desulfuricans subsp. desulfurican...
ZP_02151969  412 GRVTt-NRAARAEIWRQAYALLQDDPAWLTLYNPl-rVIGIAGTHPGF 457 Oceanibulbus indolifex HEL-45
YP_002784321 459 SLDPntPDADRTQLYSEASGIASENAYDMFICGIp-tQAAYTDKVVGI 505 Rhodococcus opacus B4
YP_002784322 456 SLDPrlDDGERTELLRRASGIAADDAYDVFICGVptiVAYSSSTVGMD 503 Rhodococcus opacus B4
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