Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_12

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cd08491: PBP2_NikA_DppA_OppA_like_12 
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: 173856
View PSSM: cd08491
Aligned: 10 rows
Threshold Bit Score: 669.084
Threshold Setting Gi: 110634300
Created: 4-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_764743     30 NVTVVLaeTVDVVEPCMaarqDVGRVIs-eNVNEMLVEFDyv-nGGLKPRLATEWSKidddTWEFKLRPnVKWHDGKPFT 107 Rhizobium legum...
YP_674508     33 SIVLAMpaEPTSVDACDdstrANARVLr-gNVVEALTRLDpq-sGAVGPLLATEWSSpdnkSWLFTIRPgVTFHDGTPLD 110 Mesorhizobium s...
YP_666055     34 AITVVLptEPDSLDPCDtq-tATNGNVskdNIFESLTKVSpe-dGTVIPLLAASWDRvepnVWHFHLKEgVKFHDGSEFD 111 Mesorhizobium s...
YP_002289058  30 DVTIVLetQPDQLDPCQssksQVGKVIk-qNVVETLTEISpe-nGKITPRLATEWKQvddlTWRFKLRQgVKFHDGTPFN 107 Oligotropha car...
NP_396005     30 DIKIVLpeEADLLEPCMatrsNIGRVIm-eNVSETLTELDvrgkQGVMPRLAEKWEQtgdsAWRFHLRQgVKFSDGKTFG 108 Agrobacterium t...
YP_002486120  45 TVRVVLgqEPPTLEACEsnltSTGVVVr-sNVTEPLIERNpq-sGELEPKLATEWKAtsdtEWTLKLREgVNFQDGTPFN 122 Arthrobacter ch...
NP_436648     28 EVKIVLpeQPANLDPCRsirsDIGRIIn-sNITETLTVIDte-kGTVGPWLAEKWEQvddlTWRVHLKSgVKFQDGAAFD 105 Sinorhizobium m...
YP_002780990  47 TLRIVLpqEPPTLEPCDasltSTGVVVr-sNITEPLVERNad-tGDLEPKLADSWEQtsdtVWTFRIRPgVTFSDGSAFD 124 Rhodococcus opa...
NP_436032     29 EIKIVLpeQPANLEPCGtiitNVGQILs-rNVVEPLTIIDpk-sGQPTPGLATEWKQtdpnTWQLKLREgVKFQDGAAFD 106 Sinorhizobium m...
YP_001632488  30 DVRIVLpeQPANLEPCGsimtNVGQVLn-qNVTESLTVIDak-tGKAMPKLATSWEQvdpnTWHFKVRQgVKFHDGADLN 107 Bordetella petr...
YP_764743    108 AKDVQFTIERNKNkklscetgg----kyfggmefsFETPD-ANTIRITTkpaqPILPLLMTvmsvesaeatpadeftrkP 182 Rhizobium legum...
YP_674508    111 AAAVAFGINRSMNpdltcqtl-------slfptktTATVEsDMVVRITTeepdPILPARIAyidlpspkt-peaaksdtP 182 Mesorhizobium s...
YP_666055    112 AETAAANIIRSQAgtdfyggalacynseqfvervdAEAID-KYTLQVSTerpdPIMPLRLTyidmgslesqqkaekitnP 190 Mesorhizobium s...
YP_002289058 108 AAAVKYSVERTLDkaidceirv----kyfggiditATPIN-DYEIEFKTktpqPILPTLMGtvvamstat-pmgkitreP 181 Oligotropha car...
NP_396005    109 AKDVKYSFDRIFSdknicesrr-----yfggmkfdVKVVD-DNTIDFKVdpvqPILPLLLSlvtivpdg--tplafvreP 180 Agrobacterium t...
YP_002486120 123 AEAAAFTIDRAVNsklgcnveg----yvfgdadldVKAVD-ATTLTVTTpepdPILPLRLSflevvptst-sttekvreP 196 Arthrobacter ch...
NP_436648    106 AEAVVKSINRLMNpgltcdsrs-----kfgdvkltPKAVD-AQTVEISSdspvPIMPTLLGtvqivspnm-pfdkesndP 178 Sinorhizobium m...
YP_002780990 125 AEDAAFSIDRTVNstigcdvdg----yvfgddalvVNAID-PSTVTVQTptadPILPLRISfvemvpstt-dtkdkvrdP 198 Rhodococcus opa...
NP_436032    107 AEAVKFSIERMTGgkltcsnia-----kfgdakltVTPLD-ELTVEIKSdkpqPILPTLLSvvmivspnt-padkavndP 179 Sinorhizobium m...
YP_001632488 108 AKAVAFSIERMTGgkltcnnma-----kfgnakltVKPLD-DYTVEIKSdrpqPILPTLLSvvmvvspnt-pvdkavndP 180 Bordetella petr...
YP_764743    183 IGTGPYTFDKWEIgQSIVLKRNPEYWGEKPQVEQATYLFRSDSAVAAAMVDAGEADIVPavsvqdatnKETDFAYPNSET 262 Rhizobium legum...
YP_674508    183 IGTGPYRFAGREIgQSITLSAFDGYWGEAPEIAEANYVWRAEATIRASMIKTGEADIAYdiptheaegQANAQQYLTNGV 262 Mesorhizobium s...
YP_666055    191 VGTGPYQFVERIQgQSIKLTRFDGYWGEIPEVKDVTYVYRTEASVRAAMVETGEAQLATairaenatgDDRTVAYKDNRI 270 Mesorhizobium s...
YP_002289058 182 IGTGPYKLAQWVPgQQIVLERTNDYWGSKPKVTKATYIWRSESAVRAAMVASGEADISPnvavqdatdPSMDFSFLNSET 261 Oligotropha car...
NP_396005    181 IGTGPYKLSNWTPgQQIVLDARDDYWGKKPAVTKATYLFRADPAVRAAMVQAGEADLAPsisqvdatnDKTDFSYLDSET 260 Agrobacterium t...
YP_002486120 197 IGTGPYKIDSWDAgQKISLSSWDGYWGNKPAYAKAEYQWRSESSVRAAMITSGEADVAMglsp-ddniGDLGVDYPNNET 275 Arthrobacter ch...
NP_436648    179 VGTGPYVVESKSN-EQIVLKRHDAYWGAKPDVTRATYVWRSESAIRAAMVESGEADMTPsiavqdatnAESDFAYLNSET 257 Sinorhizobium m...
YP_002780990 199 IGTGPYKIDYWDHgQRLSLVRNDTYWGTAPEYTRAIYQWRTEGSVRAAMVTNDEAELATylgp-edgaGDLGAAYPNNET 277 Rhodococcus opa...
NP_436032    180 VGTGPFKLSSFTP-QTVVLEAFDGYWGEKPAIAKASYVWRPESSIRAAMVETGEADLTPsiaiqdatnPETDFAYLNSET 258 Sinorhizobium m...
YP_001632488 181 IGTGPFKLTTFSP-QTVVLDPFAGYWGKKPVVTKATYVWRQESSIRAAMVETGEADLTPsiaiqdasnPKTDFAYLNSET 259 Bordetella petr...
YP_764743    263 TSLRIDTRAAPLNDRRIREAMNLAIDRQAMLGTLFpEQAKIatQLVVPttiGYNADIpa--wPYDPEKAKELVAAAKADG 340 Rhizobium legum...
YP_674508    263 FYLRPMLQKPPLDDLRVRQAIASSIDKATLAEVLMdNSGTPtgQLVTQlinGYVPDYtg--mPYDLEKAKALFAEAKAAG 340 Mesorhizobium s...
YP_666055    271 FLMRVMTHKEPFLDPRVRRAISHAVDRDSITRALMgITGSPwyQMLGPqvnGFIPDFdnsqlAYDPEKARQLLEEARADG 350 Mesorhizobium s...
YP_002289058 262 SRLRIDAAIPPLNDVRVRLALNYATDREGMKGTIFsKQVIAstQHVVPginGHNPDLkp--yPYDPAKAKALLKEAKAAG 339 Oligotropha car...
NP_396005    261 VYLRLDGNIAPLNDVRVRKALNLAIDRQAFIGTLVpQDAVLatALVPPttlGWNPDVkv--fPYDPDQAKKLLEEAKAGG 338 Agrobacterium t...
YP_002486120 276 VALRMDANEAPLNDIRIRQAVNYAIDKEGIVNSLYqGKHQVaaQLVPEgivGHNDELkg--wPFDLEKAKSLVAEAKADG 353 Arthrobacter ch...
NP_436648    258 TRMRIDAQIPPLDDVRIRKALNMAIDWDGMGEALFgKDVLRasQMVVPgvrGHNPDIkp--wTYNPEEAMKLVEEAKAAG 335 Sinorhizobium m...
YP_002780990 278 TALRMMATEPPLDDYRVREAIDLSVNRAGIVKALFqGLGDPagQLVGSsivGFDPDLqp--tPFDPDRAAQLVAEAKADG 355 Rhodococcus opa...
NP_436032    259 TAIRIDAGFAPLDDVRIRKALNLAIDWDGLAQLFGeDVQRAs-QMVVTginGHDDKLap--wTFDAEKARALIAEAKAAG 335 Sinorhizobium m...
YP_001632488 260 TAIRIDLEQPPLDDVRIRKALNLAIDWDGLSQLFGdDIQRAs-QMVVPgiiGHDDKLea--wKYDADQARKLVAAAKADG 336 Bordetella petr...
YP_764743    341 vPIDREIRIIGRngqYPNATEAMEAMMAMLQEVGLNVKLDMyDVSVWNGYFVAPFvadsgptLTQSQHDNatGDPVFTAF 420 Rhizobium legum...
YP_674508    341 vAVDTPITLVARtdlFSGAEEVSQAIQQMIQQAGFTVTLKSvDTVGWSPWARKPDsltqpvnLLTSSHNNisGDGSLTFP 420 Mesorhizobium s...
YP_666055    351 vPVDTEFLIISRpdqLPNQTEVVQAIAQNLEQVGFNFQLLNmEGSAWLKYLRAPFpddqpatLQMVSHDNtsGDASFSFP 430 Mesorhizobium s...
YP_002289058 340 tPIDREIVLVGRynlYPNSEESVQALQAMYEAVGLKVKLRMtEAAEWYKLLFKPFadnrqptLFQEQHDNnnGDAVFTIY 419 Oligotropha car...
NP_396005    339 vPVDNPITIIARtanFPNVTEIMEAVQAQLQDVGFKVELRFvEVAEHEVYYSKPFkegrgpqIVAAMHDNskGDPSFTMF 418 Agrobacterium t...
YP_002486120 354 vDTSKQISLVVRsaqFPKITELAQVLQEQLSQAGLNVKLKMlETSQHLTYQVRPFaeddgavALMTQHGNqaGDAAFTVD 433 Arthrobacter ch...
NP_436648    336 aPVDKEIVLIGRngfFPNSAESLEAMRSMWQEIGLNVSIRQlEAADWVRYLDKPFpegrgptLFQQQHDNntGDAGFTAP 415 Sinorhizobium m...
YP_002780990 356 vPVDKQIRLIGRtgqFPKINETIEVIQNSLSKAGLNVKIEMmDTAGQMQYQIRPFpqgtgpiLLMIQHGNqaGDAQFTVD 435 Rhodococcus opa...
NP_436032    336 vPVDTEIELIGRngiYPNGTEAMEAMMAMWQDVGLNVKLTMlDVNDWLRYLQKPFpesrgpnLLQMMHDNnkGDAAFTIP 415 Sinorhizobium m...
YP_001632488 337 vKVDTEIKLIGRngiYPNGAEAMEAMMTMWQGVGLNVKLVMlDVADWTRYLQKPFpaerganLVQMMHDNnkGDAAFTIP 416 Bordetella petr...
YP_764743    421 vkyaTDGshsmvrDPAVDALIAKATSaTGDERTKLWKELFAKVNTEiIADIPMFHMvGFTRVSPRLDFKPtiaTNSELQL 500 Rhizobium legum...
YP_674508    421 nflgSGGrlsvvdNAELDAKLAAAAKaSGEDRAAAYREIAQYAYDQ-ELVIPVAALqGLLLTSDRIAYEAdgfTDIELHL 499 Mesorhizobium s...
YP_666055    431 ryisCEGpvsstcNERIDELLKQADVaADEERAKLYQEAARILYLEeTSMIGVAEQaRLIRLGDGIRYDAnpmSGVIIRI 510 Mesorhizobium s...
YP_002289058 420 vkyhSQGgqstinDPELDKLIDEAGKsTGEKRTKLYQEAFKRIHEVdVPDVSLFHMvGFTRVNKRLDFRPsiaTNSELQL 499 Oligotropha car...
NP_396005    419 fkydTNGtqsgfsDKNVDDLIKRASAaTGDERAKLWSQLIAYVHDDlVADVLLFHMvGYSRVSERLDFKPtiaTNSMLQL 498 Agrobacterium t...
YP_002486120 434 qymlSTGaqsyfgTPEFDAMIKKADAaSGDDRQKAFEEIFAYQNDKvVQFAHISHQtGILGKAKSVNYTPnssSGDELRI 513 Arthrobacter ch...
NP_436648    416 vmylSEGqystiaDPDLDVVLKKAMAaTGDEREKLFQEVFAKVHDEiVADVPMYHMiGYVRVGSRLDWKPdlkTNSEIAL 495 Sinorhizobium m...
YP_002780990 436 qymrSDGyqsyfgSAGYDAQIDAAEQlVGDARQDAFASVLANEPREiRQFAYIAHMnAVLAKSPTVQYTPnsaTGDEMRL 515 Rhodococcus opa...
NP_436032    416 ifytSAGsystfsDAALDKEVADAMAaTGEDRTAKFKAIFAKVHDDlAVDIPMFHMiGYTRVGSRLEWKPditTNSEIPL 495 Sinorhizobium m...
YP_001632488 417 ifyrSSGqystlnDPAVDKEIDAAMAaTGQAREDGFKKIFRQMRTEvVPDIPMFHMiGYTRVGKRLDWKPditTNSEIPL 496 Bordetella petr...
YP_764743    501 SQI 503 Rhizobium leguminosarum bv. viciae 3841
YP_674508    500 SDV 502 Mesorhizobium sp. BNC1
YP_666055    511 ADI 513 Mesorhizobium sp. BNC1
YP_002289058 500 SLI 502 Oligotropha carboxidovorans OM5
NP_396005    499 SEI 501 Agrobacterium tumefaciens str. C58
YP_002486120 514 SEM 516 Arthrobacter chlorophenolicus A6
NP_436648    496 SEI 498 Sinorhizobium meliloti 1021
YP_002780990 516 SEM 518 Rhodococcus opacus B4
NP_436032    496 ANI 498 Sinorhizobium meliloti 1021
YP_001632488 497 ANI 499 Bordetella petrii DSM 12804
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