Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_16

?
cd08502: PBP2_NikA_DppA_OppA_like_16 
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
?
PSSM-Id: 173867
View PSSM: cd08502
Aligned: 62 rows
Threshold Bit Score: 469.362
Threshold Setting Gi: 225387021
Created: 27-May-2009
Updated: 2-Oct-2020
Structure
?
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
YP_001756901  28 TLKFIPqadltvLDPIWTTayVTRNHGlAVFDTLYGTDAgYAAQPQMVAGHTVen-dGKLWRLTLRPGLTFHDGSPVLAR 106 Methylobacteriu...
YP_522260     31 AIVAITqap-ptLDAQVTTiqSARHINlHIYETLYARDEnGKPVPDLAESVAIsp-dGKTYTLALRKGVKFHNGKTMGSA 108 Rhodoferax ferr...
YP_002522726  77 TLRVAIigeppaLDPQFTTatITANITwHMFEALFYRDKqFSPKPLLTESYEFte-nNKVLTIKLRSNVKFHDGRPLTAD 155 Thermomicrobium...
YP_001630192  40 TIVVATigepptLDPMASTadLVGILTqHIFETLYTFDAkWNATPLLAEKLPQvsddGLTYTIALRQGITFHDGSAMDSA 119 Bordetella petr...
YP_001033852  34 DLIVAQasnppsLDAMVTTsqMSRNITmNIYETLYGFSDsIVPIPILATGVEIse-dGLTYRFPLRAGVKFHNGKEMGAE 112 Rhodobacter sph...
NP_766948     35 LLREATigepppLDVMLTTadVASVIGrHIFETLYALDSaYTPRPMLAESDREed-gGKTIVIKLREGVPFHNGKEMTAR 113 Bradyrhizobium ...
CAP64353      68 NIAVVAep--pgLDPMISTadLVGTIMqHVYEPLYTVDArWNLAPMLAEAMPAisedGKVYTIALRKGVKLHNGRDLDAD 145 Bordetella bron...
ZP_01227963   35 IITVATigepntLDPMAATgdLLGMVTqHFLETLYTFDKeWNVTPLLAADMPEisddGKIVTIALREGIKFHNGKTMTAD 114 Aurantimonas sp...
ZP_01747472   38 TIDVAIigepdtFDPMVSTkdVVSIVTqHFVETLYTFDDtWSVVPLLAAGMPEisedGLTYVIPLREGVTFHDGSSMDSA 117 Sagittula stell...
NP_357336     28 VINVATigepptLDPMASTadLVGIVTqHIFETLYTFDKgWKVTPLLAESLPEisadGKTYTIKLRQGIKFHDGSDMTSE 107 Agrobacterium t...
YP_001756901 107 DCVASVARWGKrdamGQTLMayt-deLSAPDDRTIQFRLKKPFALLPDALGkvgssicAIMPERLArtdpf--tqvteMV 183 Methylobacteriu...
YP_522260    109 DVVASLERYRKig-aNANLLsev-etISAKGPNEVVIKLKKVQSTLLDTLSsst-aplAIYPAEEAakga----nkiaYI 181 Rhodoferax ferr...
YP_002522726 156 DAIASLLRYSKlsgrGRNLFtrv-anLDKVDTHTIRFEFKEPTGIALIYLAqv---dsFIMPKDLAeaypd--kgleqFI 229 Thermomicrobium...
YP_001630192 120 DVVASLKRWTEtasrGKQAAkli-saIEAPDAHTVRIVLKQPYAPLTALLAmnn-saaVVMPREKLatp------lkeFI 191 Bordetella petr...
YP_001033852 113 DVRASLERYKAi--gGTASMlagvtsIEASGPLEVTLTMEKPFPGFLEAFAspr-apaVIIPAEEAgkpa----neiaVI 185 Rhodobacter sph...
NP_766948    114 DVAASLTRWGNfgarGKLLMaaa-tsVEATGKYEVTLKLSAPNGAWKNLIAdvn-gglAIYPEEIAanagnrpieqkdYI 191 Bradyrhizobium ...
CAP64353     146 DVVASLQRWLDisprGKAVKlev-esLSAPDPATVRIALKAPYAPLVSQLAats-gmaAIMAKESLgpq------vteII 217 Bordetella bron...
ZP_01227963  115 DVVASLERWLKiasrGQLVAdkv-ekVEAVDANTVKISLSAPFGPLPALLAfnn-saaVILPKEILaep------lieFI 186 Aurantimonas sp...
ZP_01747472  118 DVKASLDRWLEvasrGKAIAdkv-ssVEATGPNEITLTLSAPYAPLMSLLAfsn-saaAIYPEEIIape------ietVI 189 Sagittula stell...
NP_357336    108 DVVASLGRWMKiasrGKQAAgfi-dnISAPDAGTVTITLKQPYAPLTSLLAfnn-saaIILPAEKQaep------maeFV 179 Agrobacterium t...
YP_001756901 184 GSGPFRFKADERvvgARVVYERFAGYVPRegge-pqwtSGPKRAFVDQVEWHVIPDqaTAASAMQTGemDWWEqp---pa 259 Methylobacteriu...
YP_522260    182 GTGPFKFVEFIPd--SHVKLERFKDYVPNphytkrdgfAGKKEVYLDTVTFRFMPEagARVAALQSGevQLVEt-----v 254 Rhodoferax ferr...
YP_002522726 230 GTGPFKFKERLPd--RYIALVRNEDYTPVdggp--dgyGGTKIPYFDEIRFIPVPEqaVRGDGLVTGefDFAEqlsldny 305 Thermomicrobium...
YP_001630192 192 GTGPYQLKARVPd--QYIQLTRFDGYRARdgep--dgyGGARKQYLDEIRFAPVSNanTRVESAAAGqyDYVDal---pv 264 Bordetella petr...
YP_001033852 186 GTGPYKFVEYVPd--SHVRLERFADYAADethadidgfGGKKTAYLDSVTFRVIPEpgAAVAALEAGevQLLEqipvpta 263 Rhodobacter sph...
NP_766948    192 GTGPYKFVEWRPn--RYVEVEKFDGYKPVkekg--dgfAGARIAIFDKIRFIPVPDvgTRVSGVQAGdyDYAEmi---sg 264 Bradyrhizobium ...
CAP64353     218 GTGPYRFKERRPd--QFVVLVRFDGYHPRteap--sgyAGRREALLDELRFIPVPSpnTRVEGALSG--QFHFs------ 285 Bordetella bron...
ZP_01227963  187 GTGPFMLKERRPd--QYIQLVSFPDYKPLdgda--dgfGGRREALLDEVRFVPVPDanTRVEGAVAGqyDFAEllpvesy 262 Aurantimonas sp...
ZP_01747472  190 GTGPYKLEAHQPd--QYTQLVRFGGYTQPt-------gAAERAQTPDEIRFIPVPDgnTRVEGLLSGqfAYADglsteay 260 Sagittula stell...
NP_357336    180 GTGPYMLKERKAd--QYIQLVRFDGYKSRdges--dgyGGARHQYLDEIRFVPVPDpnTRVEAAVSGqyDYVDsi---pv 252 Agrobacterium t...
YP_001756901 260 DLVP-----TLGglt---triTDPTg---lIGCLRMNql-qPPFDNPAIRQVLLKVVDQTDFMQAVTGtdpklihvpTGF 327 Methylobacteriu...
YP_522260    255 DGPTk---kRLEtnpa-fkiyKLLPf---sFQIIKLNha-vPPTDNLAFRQAVVATLDMEEIMSIAYPdiyq-ldggWLY 325 Rhodoferax ferr...
YP_002522726 306 DAFKaepnlALQ---------VTLPy---yFYGAHFNkskeSIMSNPKLRHALLAAVDVEPVARAGFSrpe----fyRLY 369 Thermomicrobium...
YP_001630192 265 ESIA-----KLKngrs--dpmLLKPf---gWPRLVLNtk-qGIMSSLPARRAVQLALNEEDMLYAAFGnkdfyaldaDLY 333 Bordetella petr...
YP_001033852 264 RRLAgn--sEMK---------VYENsp-waFLVFIFNln-eAPADNPKFREAVQIALNSEEIMAIATEgl------fNLY 324 Rhodobacter sph...
NP_766948    265 DLYE-----SLSkdq----svQVQRtnasiFGLFFMNskqgILKDNYKLRRAIQTALDKSQALRVAFGskdlwnaegSIF 335 Bradyrhizobium ...
CAP64353     286 DQLSvesaeRLQasgsvavpvIIQDf---gFPYIVLNsk-qGVLVSQAMRRAVQAAVNNRELMDAGFGdkrfysvgpNFF 361 Bordetella bron...
ZP_01227963  263 DRLTg----QTEp--------MLTEsf--gWPMFIMNtk-qGVMTDQDMRKAVQSLQNSDDLMLAAFGeerffkvdgAMY 327 Aurantimonas sp...
ZP_01747472  261 DRIAea--aGAEp-------vLLEPf---gWPVFAINhk-kGLMTDLNIRKAVQAALPFDDMLFAAFGdekffqtdgAMY 327 Sagittula stell...
NP_357336    253 ESFE-----KVKsssa-sqpmMLKPf---gFPVFVFNtk-eGLASKLEVRKAVTEALNMEDMLAAAFGstdfyaldgAYY 322 Agrobacterium t...
YP_001756901 328 FCpg---lPMASDVGldvl--trkRDYAGAKAALAAAGYKGeKVVLMGASDfpslKALADVAADMLTRAGFNVDYQvmDW 402 Methylobacteriu...
YP_522260    326 PKs-----PAYVGVGlnt---ynkPDLKKARELVVKSGYKGeKITFLVDNLra-nTDTATVVQQRLAQIGVNVDIKvtDW 396 Rhodoferax ferr...
YP_002522726 370 SSqsapetPWHTDGGaey---ynqRNPEKAKQLLAEAGYDGrPIRWLSTKEysynYNMALVLKQQLEAIGVTIDLQvmDW 446 Thermomicrobium...
YP_001630192 334 PQg----yPWATQLGgkv---ynqGDAAGAKKLLDEAQVQDrTLRILTSQQyefhYKMALVAAEYLKAAGFKVDMQvvDW 406 Bordetella petr...
YP_001033852 325 HGwm--yeGTTYDAGeigkdrynvADLDRARALLAEAGYSGqPFTILTDTQgperNKAAVVIAEQLRAIGVNVVINqvDW 402 Rhodobacter sph...
NP_766948    336 PKg----tPWYSAEGvsg---yspHDPKKAKELAKEADYTGtPIRLLVSTNyqahYDEASVFTRQLADAGINVQMMvvDW 408 Bradyrhizobium ...
CAP64353     362 PEg----tPFYSMAGael---ydnNNPKMAKEMAAQAGYKGqPIRILASRQygfhYNMALVFAEQLKKAGFKTELQivDW 434 Bordetella bron...
ZP_01227963  328 PEg----yVWRNEAGvea---ynqGDVEQAKSLAEKAGYDGePIRILTSRQyefhYKMAQVLDAYLKSAGLKSQLDvvDW 400 Aurantimonas sp...
ZP_01747472  328 PEg----wAWRTDAGvel---ynqNDQEKAKGYLEEAGYDGsPLRILTSRQyefhYQMAEVARMALEMAGFTVEMDvvDW 400 Sagittula stell...
NP_357336    323 PDn----fSWHTEEGvdgn--ynvGNPEAAAEKLKAAGYNGePLRILTSRQyefhYKMAQVAAEYLKLAGFKVDMQvvDW 396 Agrobacterium t...
YP_001756901 403 GSVVQRRAKkepvaqggWSAFCTFWagld---qanPAVSAFlrgtg--qsaaiGWPTSEKIEALRDQWldapDTAARKRL 477 Methylobacteriu...
YP_522260    397 PTAVKIGWSpe-----gWNLFAHGFgi-------qPFEGPGtvmsaw-aggqlHQKPDAEIDRLYAAYsgelDAEKGKTL 463 Rhodoferax ferr...
YP_002522726 447 ATLVKTRSQrd-----aWDIFITGHesy-----qhPVLQPYmnp------twpGFWENAQRDQLVQQLmgetDETRIKEL 510 Thermomicrobium...
YP_001630192 407 ATLTQRRQDpa-----lWDIFITHSpfl-----pePALIDFpsk------dspGWWDTPRRNQALDAFnqasNPEERVKR 470 Bordetella petr...
YP_001033852 403 PTALQIRLQdt-----gWSAWTLTMgi-------ePYLGPEalistfagpathFRKADPELDALYAELvdtaDLTARKAV 470 Rhodobacter sph...
NP_766948    409 ATLLKMRGQpe-----qWDIFVTHHsfs-----pdPLLLTFlna------sypGWWDSPEISSLRAELikstDPTARKST 472 Bradyrhizobium ...
CAP64353     435 ATLIQRRADak-----lWDIFFSHAnsq-----pePMLAPPqfss-----gapGWWESDAKKSVLGKFnaatDPAERSAL 499 Bordetella bron...
ZP_01227963  401 ATLVQRRADpa-----lWDIFITHSpflpdpaliaPLPASYp-----------GWWSTPEKEKLLTALntetDLEKRQAI 464 Aurantimonas sp...
ZP_01747472  401 ATLAQNRDNpd-----lWDIYITHSpfl-----pePALTSSffat-----areGWNNPEKNAILDRFTse-sDPEKRKAV 464 Sagittula stell...
NP_357336    397 ATLTQRRADpk-----lWDIYISHSpfl-----pePALMGAlst------sspGWWDTPARKAAVDAFtseaDPEKRLAL 460 Agrobacterium t...
YP_001756901 478 AGELQQQAFVdLPYLPLGQYfnQTSYKP-SLTGV 510 Methylobacterium radiotolerans JCM 2831
YP_522260    464 FASFQQHMINdVIAIKVGNYglFQVGTA-KLRNF 496 Rhodoferax ferrireducens T118
YP_002522726 511 ARELDRVWWEdAVMIKVCEGatLRGYTK-KLQGY 543 Thermomicrobium roseum DSM 5159
YP_001630192 471 WADVQQAVFDeVPFIKVGDFn-SLAAKSpALQGV 503 Bordetella petrii DSM 12804
YP_001033852 471 FARIQQRLDTfAPVIKLGETglMQASSA-KVEGF 503 Rhodobacter sphaeroides 2.4.1
NP_766948    473 WDKIQSLIYDqVPVMKVGDAy-TYDIASpKLKGL 505 Bradyrhizobium japonicum USDA 110
CAP64353     500 WGSVQKLVYEeVPFLRVGNFn-SLAARSnQLEGL 532 Bordetella bronchiseptica 253
ZP_01227963  465 WSDIQGLIYEqAPFYKVGDFa-ALAAKSpKVEGF 497 Aurantimonas sp. S185-9A1
ZP_01747472  465 FAELQKIVLEdVGLIKVGNFn-ALQGKAaGLEGV 497 Sagittula stellata E-37
NP_357336    461 WANVQKTIYAeLPLIKIGDFn-AAAAKSnKLEGV 493 Agrobacterium tumefaciens str. C58
| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap