Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_1

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cd08508: PBP2_NikA_DppA_OppA_like_1 
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: 173873
View PSSM: cd08508
Aligned: 11 rows
Threshold Bit Score: 578.953
Threshold Setting Gi: 221369049
Created: 27-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_551131     35 VLSISSdatdisTLDPHRattsdDKGVAsqvFNGLVRFPPGsa--dpKELQPDLAEKWQSspdkrTWTFYLRKGVQFHGg 112 Polaromonas sp....
YP_914049     34 PIRIALaatsprAIDPIFstlgaDNWVNlqvYEHLVSPPNGrfatqdDEYRPMLAESWTKsddarTWTFKLRRDVAFHG- 112 Paracoccus deni...
YP_002540070  33 TLTLGAaandvgTLDPHYatstsDRTLVawiYGALVRFAPGst--dpATLEPDLAESWQSsddklVWTFKLRSDVKWQA- 109 Agrobacterium v...
YP_551122     31 ILRIGSdaiditTLDPHRtavseEKGLIsmiFGGLVRFPPGsa--dpEKIEGDLAESWQAsadglTWTFKLRHGVQFHRn 108 Polaromonas sp....
NP_059749     33 ELSMGVasedvtTLDPHFatttsDRTLVsyiYGALVRFAPGsa--npSSIEADLAESWESnadqlVWTFKLRPDVKWQGg 110 Agrobacterium t...
YP_001967428  31 TLRVGAaaenvaTLDPTRatatvDVGVVswmFNGLVRFPPGsa--dpTKIEPDLAEKWETtpdglVWTFHLRNGVKFHGd 108 Agrobacterium t...
ZP_02190633   24 TLNVGSatadagKLDPHLatttpDKGLLhwmFNGLVRIKPGra--spGDIEPDLAESWTAsedglTWTFKLRQGVQCHGk 101 alpha proteobac...
NP_746569     35 TISVSPgiaditSLDPHRaslvgDKGIVaemFNALVRFPPGss--dpAALEADLAERWESsddkkVWTFFLRKGVMFHGg 112 Pseudomonas put...
YP_002520145  39 ILRIRNdgd-irRLDPATrggwyDETVMfsiFSGLVRYKAGd----aWGWELDAAESIDDsd-pqHVKFTLRPGIRFTG- 111 Rhodobacter sph...
YP_675165     36 RTLSIRisreiqNLDPPFmagttDSNIIravFQRLVSYIPNs-----YEYELDAAESIEQvs-plQIDFTLKKGQMFTDg 109 Mesorhizobium s...
YP_675175     35 SFIARVdrd-veNLDPAFrtsltDSNVIrvvYQRLIDYNVGa-----YGWQLDAAEAIEQks-dlEITFRLKQGIMFTGg 107 Mesorhizobium s...
YP_551131    113 YGE-VKAADVVYSFMRAADkg----rSSFAANFeviekVEARDDYTVRFLLkyp-daAFLGRVsNYHAGni--vsQAAAE 184 Polaromonas sp....
YP_914049    113 GHGtLTPEDVVFTFERAMRegi--atASYANVRg----VAASGPDEVTFTLngp-dpFFLGGViSIPSSli--vcKSAVE 183 Paracoccus deni...
YP_002540070 110 GYGeVTADDVVFSLDKARDpk----rSAFSADFaafdkVDAVDPHTVRITLsrr-vpNLLGLVtNYAGGfi--vsKKAFE 182 Agrobacterium v...
YP_551122    109 YGE-VNAEDVVYSLMRAADpk----rSSFSSTFepvkeVSALDSHTVRIQLkap-vpSLLGLVaNYHGGmv--vsRKADQ 180 Polaromonas sp....
NP_059749    111 YGN-VTADDVVFSLDKARDpk----rSAFSGDYaaiqkVEAVDAKTVRITLtrr-vpSLLALLsNFSGGfi--ipKKAFK 182 Agrobacterium t...
YP_001967428 109 YGT-VTSEDVVYSLERAKNpk----tSSFSNDFtevksIEAIDPLTVKITLnsp-vpGFLGLIaNYHGGni--isKKAAE 180 Agrobacterium t...
ZP_02190633  102 YGE-FDAEDAVFSINRASNkd----sSSFSKDYaalksVEATGKYEVRITLanp-vpSLLGLLvPYHGGnm--vcKDAVE 173 alpha proteobac...
NP_746569    113 YGE-LKAADVVYSLQRAADpk----rSSFSANFtalekVEALDDYTVKVTLkyp-dtAFLGRVsNYHGGqi--vsKAAAE 184 Pseudomonas put...
YP_002520145 112 GFGeMTAEDVKFSYERFRDpe---vnAVYGADWaaldhVEVTGTHSGIIHLsrpfapLFASTL-PHASGlilsraAMEAA 187 Rhodobacter sph...
YP_675165    110 YGE-MTADDVKFSFERYITpdadgrvSSYKEDWsalveVQVHDTYSGSIILskp-spSIWGVIfTGSSGai--qsRKAVA 185 Mesorhizobium s...
YP_675175    108 YGE-MTADDVKFSLERFAFpdaegrvSSYRQDWadlkeVVVHDKYSGSIIFerp-apNIWQSAlPHASGai--vsRKAVE 183 Mesorhizobium s...
YP_551131    185 KLGDRFgqsPIGTGPFAFSEHVTqQYVKLVANDAYFrgAPKLAAITYRMIPsdsARELAFTSKEVDMMSgkreqrwv--- 261 Polaromonas sp....
YP_914049    184 EKGENFgkePVGTGPYAVERMSS-SGVNTLRFDGYWgePPKTARIDFLYTSdttSRTLSLMSGDVDMIEavrapgwvq-- 260 Paracoccus deni...
YP_002540070 183 ERKEGFaraPVGFGPFEVKSIVAgQNVSFVANKDYFrgAPKLSTLNYRFINnnaSRDLAFVAGEIEAAAglanknwlq-- 260 Agrobacterium v...
YP_551122    181 DLKDAFklkPVGFGPFEFVEHQKqREVVLKAHDKYFrgKPKIERIVYRFIPseaVRGLAFATGELDLVAgqrdqrwvqra 260 Polaromonas sp....
NP_059749    183 ERGDDFkrrPVGFGPFQVESIQPgQSVTLTANAEYFrgKPKLSKISYRFLNneaARDLAFESGELDVEQgnqdqrwlq-- 260 Agrobacterium t...
YP_001967428 181 KLGADFklrPIGTGPFMFENAVTqQSVTLKAFSDYFrgKPKLDGIQYNLIPsdaSRELAFRSGELDLIYgkreqrwvd-- 258 Agrobacterium t...
ZP_02190633  174 DLGAQYertPIGTGPFMFAEYQPqQYVKLVANDAYFrgAPKLKEIYYRYIPsdaSRDLAFQSGEIDMIYgkqdqtwve-- 251 alpha proteobac...
NP_746569    185 KLGERYgqaPIGTGPFAFSEHITqQYVKLVANDQYFrgKPKLGAIVYRMIPsdsARELAFASDELDLMLgkreqrwv--- 261 Pseudomonas put...
YP_002520145 188 GRSVIDtdpLACSGPYQIAEWRPrELIHLVRNPGWVgpAPHFDEIRLLPLTdliSAETAFDAGDIDVTQiavnsi----- 262 Rhodobacter sph...
YP_675165    186 ALGKEHsrkPIGSGPYMVSAYEDhRGVTLVRNPEFTayTPDFETCNLVYIAnqkTAEVALRAGEIQFTElsvdsade--- 262 Mesorhizobium s...
YP_675175    184 KFGAQFgrnPVGSGRYEVVSFSAqDGVVLKRNPLFLdtPGEFESFTVRFISnvkTAQLAVEAGEIDFTQvplttvpe--- 260 Mesorhizobium s...
YP_551131    262 ----dgaskrgmKVD--VFDPa-EFRTLHINrtikPLDNLKVRQAIAAAVNVDEILRYVGk-SVGDKg---cSIIPNGYL 330 Polaromonas sp....
YP_914049    261 ---qirqqndalIVD--QTQPg-SFNTLFFNltkaPFDNPLVRKAVATAIDSAVVAQALAp-FGAQTwtlspPDYPSGWA 333 Paracoccus deni...
YP_002540070 261 ----rteplpgaVID--VFYPa-EVSLLHINitkpPFDDIRVREALAYAVNPQAVVEFKGarFTTRPt----SVVPSNNL 329 Agrobacterium v...
YP_551122    261 rlwappkdqssvKVD--VFGPg-EFRTLMLNrrikPLDDPRVREAVARAVDVQELVHFVGa-DIVKPg---rSVIPPGYA 333 Polaromonas sp....
NP_059749    261 ----rltanpenVVD--TIEPa-ELNLLHINitkpPFNDIRVRQALAHTVNAAQIAKYRGe-RVNRAv---pSVIPSNNL 329 Agrobacterium t...
YP_001967428 259 ----qakawdgsTVD--IFAPg-EYRTLFLNqahkPLDNVKVRQAIAHAVNVDQIVEFVGa-GVGQKg---cSVVPPGFL 327 Agrobacterium t...
ZP_02190633  252 ----riskipntTVA--VMEPg-EMSVLSLNmtmpPLDNLKVRQAVAHAIDRDTMVKFKGe-AVTRPs---vSVVPEGYL 320 alpha proteobac...
NP_746569    262 ----ersrargvNVD--VFEPa-EFRTLFLNrnikPLDDVKVRQAIAASVNINEIIRYAGk-DVADGg---cSIIPNGYQ 330 Pseudomonas put...
YP_002520145 263 -------avrdaEADnlVVKPalAYTWLGMNieneVLQDLRIRRAIQHAINTREVVEGTFgeAVTPAh----GLIPPPLL 331 Rhodobacter sph...
YP_675165    263 -----magidgvVVD--KRPGq-RFIWLGMNmqkaPLDKLAVRQAIRAAIDVEQMVLAGYq-GNAQRl---nAMIPPGLL 330 Mesorhizobium s...
YP_675175    261 -----lersgrvAVS--VIPTq-KFIWLGLNtespKLADIKVRQAIRAAVNIDEVLLGAYq-GKAPRl---nTLLPAGLA 328 Mesorhizobium s...
YP_551131    331 GEdcsa-ggytYDVARAKKLLTEAGFpn--giSIKSVVSnvs--aqQPIMQIVQSQLAKAGIKLEMEvvDHATYQAKSRK 405 Polaromonas sp....
YP_914049    334 AEdlpedlrydYDPDRARELLAEAGHg----nGLNFTASisqredyRSIMLILQELMRPAGINMNLNimDHAAFHGANRQ 409 Paracoccus deni...
YP_002540070 330 GYlkda-gvfpYDPAKAKALLKDAGFgd--glTFSMLSSqlp--eyETTAQVLQGQVEDSGIHMQLQpvEHASWHQMIRK 404 Agrobacterium v...
YP_551122    334 GEvdvg-pkfpYNVGKSKALLTEAGYan--giTLRAVVSsta--sqLSVMDVVQKQLKRAGINLTMDvvEHAAYHAQIRK 408 Polaromonas sp....
NP_059749    330 GFdpda-gvlnYDPAQSKKLLAEAGFpn--gvTVTMVASqlp--glESLAQLIQAQVAEGGFTLNLQpvEHAAWHQMIRK 404 Agrobacterium t...
YP_001967428 328 GEdctw--sykYDPELSKNLLTEAGLgn--glTIKAIVSsaa--aqQPIMQVVQGQLSEVGINMDMQvvDHATYQEQSRK 401 Agrobacterium t...
ZP_02190633  321 GYtddv-pqypFDIAKAKALLAEAGFp----dGVTIKAIhttlpgmLSTIEAVQALLKEANINLEITtvEHATFHAQIRK 395 alpha proteobac...
NP_746569    331 GLdcsa-gpyaYDPAHAKALLASAGYpn--glKLKSVVSnaa--pqLPIMEIIQAQLAKAGITLEMEvvDHATYQAKSRQ 405 Pseudomonas put...
YP_002520145 332 GArean--lygYDPDAARALLAEAGApal-qlTLSFNGDpd----mMIAAQVIQAHLAAVGITLEIRamDGATLTAQQQD 404 Rhodobacter sph...
YP_675165    331 GHwada-pvyqRNVDEARQLLASAGValpltlKLTILNEpa----fQNMGLVAQALLQEVGINIEIDqrEAGTFWSSGKG 405 Mesorhizobium s...
YP_675175    329 GHwaea-pvytQDLQQAQALLAEANVsgplkvKLTVLNEpv----fNTIALIVQAQLAAAGIEVEIDqrEGGSFWSAGKD 403 Mesorhizobium s...
YP_551131    406 Dqs----aLVFYGAARFpia-dvWLTEFYDsaasigap----kaisnfsHCSVGDDAIRQARiepDAQKQLALWKQAQQK 476 Polaromonas sp....
YP_914049    410 Dan----sLVLYSQSLPpvpleyMSRYLSSaavvksdgtggdnfshygiAMPGVDDRIEAMRqatTVEEYSSIGREIEKK 485 Paracoccus deni...
YP_002540070 405 Dls----pVVLYGAARFpia-diFLTQFYDsasivgqp----gavtnfsHCNVADKQIREARteiDPAKQIALWQEAQRL 475 Agrobacterium v...
YP_551122    409 Dvs----aIVFYGAARFpva-dsYLTEFYHsrseigap----tqvtnfsHCNAADKEIDAARatpNAAARSSLWRVAQVK 479 Polaromonas sp....
NP_059749    405 Dls----pIVLYGAARFpia-dyYLTQFYHsaseigkp----tqvvnfsHCNVADKQIEAARtetDPNKQIELWKEAQKL 475 Agrobacterium t...
YP_001967428 402 Dls----dIVFYGAARYpva-dsYLSQFYHsnasigkp----tavtnfsHCDAADAEIEAGRkaaTDPQRLKAWSGAQHK 472 Agrobacterium t...
ZP_02190633  396 Dls----qVVHYSAARFpia-dvYLTQFFDsastvgtp----tavtnfsHCDVADKEIQAARvepDPKKQLELWKTAQQK 466 alpha proteobac...
NP_746569    406 Dqs----aIVFYGAARYpga-dyWLTEFYDsasaigap----aamsnfgHCSVADDAIRKARveaDPQTQLDLWKKAQVQ 476 Pseudomonas put...
YP_002520145 405 SeggtykdIQLFFSTFTtapdpsWVTEWFTcaqigd-------wnfqrtCSDEWDSRNAAAAeesDPTSRAATYVDLQNQ 477 Rhodobacter sph...
YP_675165    406 Esg---eqLELFILRFNanpdptYNARWFLpnqigd-------wnwqrwDSPEFARIQEESGrnlDRESRVKQIIELQKL 475 Mesorhizobium s...
YP_675175    404 Esg---enMELYITSFNtsvapvANTRWFLpnqigd-------wnwsrwNSPEFEELYDSISvdfDIDSRSAKLIEMQRL 473 Mesorhizobium s...
YP_551131    477 IHAdVCSVPLFGLkqVWVHSDRVNYGY 503 Polaromonas sp. JS666
YP_914049    486 VQEdLPLMGVGNLgyAIVRNPAVDIGY 512 Paracoccus denitrificans PD1222
YP_002540070 476 ILKnVCAIPITETsqVWVHNQKLKWGF 502 Agrobacterium vitis S4
YP_551122    480 INAdLCAIPLFDLqqVWARRGALDYGV 506 Polaromonas sp. JS666
NP_059749    476 IVSnVCAIPLTENlgTWARKNKLGWGF 502 Agrobacterium tumefaciens
YP_001967428 473 IYDqVCGIPLFNLmqVWVRTNELDYGY 499 Agrobacterium tumefaciens
ZP_02190633  467 IMAaVCAVPVYQNlqLWAWKSNLDLGV 493 alpha proteobacterium BAL199
NP_746569    477 IHDdVCAIPLFGLkqVWAKAASVDYGY 503 Pseudomonas putida KT2440
YP_002520145 478 LEEtGAYVFLMHGvnAWISKPGIRTAY 504 Rhodobacter sphaeroides KD131
YP_675165    476 MDEtASMVWLTNDvfALGYQASVQPAV 502 Mesorhizobium sp. BNC1
YP_675175    474 MDEsAAFIWLTSDvvAYAHQTWLVPMI 500 Mesorhizobium sp. BNC1
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