Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_17

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cd08503: PBP2_NikA_DppA_OppA_like_17 
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: 173868
View PSSM: cd08503
Aligned: 93 rows
Threshold Bit Score: 353.801
Threshold Setting Gi: 38234705
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:
CAB01955      57 PVKGGILRAGLvggestNSLDPATwas--qvPYTFGrcwGEQLLEVSp-AGEIEYRLAESYEASkdakTWAFTIRKgVTF 133 Sinorhizobium m...
ZP_01034933   62 GKTGGVLRVASrv---mDITDPRKyawsepgNLARQf--CEPMVRWAs-DFTFQPMLLEAWEVSddakTYTLKVRQnAVW 135 Roseovarius sp....
YP_764646     61 MPKGGNLRIGMrc---mEIKDPHLadfaeksNVIRQv--CEYLTLTDr-NNITHPYLLEKWEVSddlkTWTLHVRKdVKW 134 Rhizobium legum...
NP_107690     70 GAPGATIRVGSsv--paATIDPVTiad--agGLLILqqvAEFLCVDGp-DLVLKPALAESWKPNdngtVWTFKLRKgVKF 144 Mesorhizobium l...
NP_103659     67 ATAGGTVRVGLgq--ptKAIDPVTitdpasiGVISQv--GEYLILDDp-KDGLQPKLALSWEADetakRWTFKLRPgVKF 141 Mesorhizobium l...
ZP_02884706   71 TPSNQTIRVAHlt--paGAVDPLTvtd--aaSLALLnqtGEFLIDDDgeKLVLKPALALSWKPNdkgdVWTFKLREnVKF 146 Burkholderia gr...
YP_001235197  64 GGEGATIRVSIta--psTAINPVVagd--tgSLCMLqqaGEFLLFDNpkTLRLEPMLATSWKSSrdgrVWTFTLRKgVKF 139 Acidiphilium cr...
ZP_02191729   64 GTLGGSFKFAMav---qEMTDPATfdwtqksNVARHi--VEYLTITGa-DNVTRPYLAESWSASedlkTWEFKLRKgVKW 137 alpha proteobac...
NP_108411     63 SKKGGTLRVAMsv---kAQKDPRTydwtemaNVTRTw--LEPLVRYTr-QFTFEPVLLESWDVNddatEYTLHLRKgVTW 136 Mesorhizobium l...
NP_105385     58 PKKGGTLRVAMnv---kGFKDPRTfdgvemsNVARHc--NEYLVRWNt-DFSFEPWLLEKWEMSddakTLTLHVRKgVTW 131 Mesorhizobium l...
CAB01955     134 HNGKELTPADVVATFERHADknsksaal-------------------------pfvqefetIKADGDKVVITLRq-PNAD 187 Sinorhizobium m...
ZP_01034933  136 NNGDAFTADDIIYNLNRWCDkavegnsmasrmgt--------------lidpetnkaidgaIERVDDFTVRLNL--PRPD 199 Roseovarius sp....
YP_764646    135 RKGRPLTADDVIWNLKRVCDpaigssmlglftgylmqeyetgekdekgnpkkssklwadnaIEKVDDHTVRLNCssPQIA 214 Rhizobium legum...
NP_107690    145 HSGGEMKADDVVASIDRLADpanssnalsv----------------------ftgilqkgaTKKVDDYTVEFHLdaPNGN 202 Mesorhizobium l...
NP_103659    142 HDGRTVTAKDVVASFERLVDpasgssalsa----------------------ykgilskggAKVVDDETVAFDLdqSNSN 199 Mesorhizobium l...
ZP_02884706  147 HDGQPFTAKDVVATFDRLADpasgsaalsv----------------------lkgvlskggAKAVDDHTVAFHLdaPNGN 204 Burkholderia gr...
YP_001235197 140 HSGGTMTADDVVYSLARLADpkngsnalst----------------------fkgvlkpegVVKVDDHTVAFHLeaPNGN 197 Acidiphilium cr...
ZP_02191729  138 NNGDDFNADDVVHNFTRWLDpktgssnvglfdamvdavdt--gekndkgkpiikktmtpgaVEKVDSHTVRLHLnsPVLS 215 alpha proteobac...
NP_108411    137 NNGDAFNADDVVSNLNRWCEkgasgnsmaarvga--------------lidpksgkakdgaITKVNDNTVKLKL--SEPD 200 Mesorhizobium l...
NP_105385    132 SNGDAFNADDVVHNLTRWCEagvagnsvaarmga--------------lvnadtkkavdggIEKVDDYTIKLNL--PKPD 195 Mesorhizobium l...
CAB01955     188 MPFIvsdyhlmiqp------nggkddptaGIGTGPYKVVVNEPg--VKHVGERQDGYWgaaeRGHADQIEITVi-nDATA 258 Sinorhizobium m...
ZP_01034933  200 ITIIagmsdypalcvh-ssfgedgdlakaPIGTGPFELVSIEIgvaAEYKRRENGKWWg--gDVYLDGIRFIDfgeDNAS 276 Roseovarius sp....
YP_764646    215 VPEHlyhypmfiid-----peengafgadANGTGPFVITEYVVg--KGAKYKARTDYWg--tGPYLDTFEYVDlgdNPGA 285 Rhizobium legum...
NP_107690    203 FPYMvssdnynavii---pasykgdyeksFDGTGPFKIEKYTAk--VGASFVRNEDYWg--eKALPERTEFTFf-aDMQP 274 Mesorhizobium l...
NP_103659    200 FPFYvssdvynaviv---padyagdfektFNGTGPFKLESFRPk--QGASFVRNPDYWg--dKALPDRVEIKFf-dDEQA 271 Mesorhizobium l...
ZP_02884706  205 FPYYvssdnynavil---panyaggyeksFIGTGPFKLEKYQAk--VGASFVRNPDYWg--eKALPQRVQFSFy-aDQQA 276 Burkholderia gr...
YP_001235197 198 FAYLvssdnynaiilp--kgsvaadyektFDGTGPFRLDAYTPg--RGASFVRNPAWWggkvMPARTEFGFYS---NQQS 270 Acidiphilium cr...
ZP_02191729  216 IPENlynyptaivhrk--fdemganlsknPIGTGPYELTKFAVg-sQAILTKRKDPYWg--gEVFLDEIHYIDlgeDASA 290 alpha proteobac...
NP_108411    201 IAIIpgftdypalvvhrdfdkdgadpikkPIGTGPFELVSYAVg-aKAVVKRRENGKWwg-gEAPLDSVEFTDygtDFNA 278 Mesorhizobium l...
NP_105385    196 ISLIagmadypalimhrsyagdgdpmkalAITTGPCELVKWDAe--TGAQVKRKDKPWwk-gEFHLDGIQWIDygsDPNA 272 Mesorhizobium l...
CAB01955     259 RTASLQAGgvHIINriepkivalVKRIPGVTIRNVPGkgHYVLIAHcn--taPFDNNDLRLALKYAVDREEMVAKILaGY 336 Sinorhizobium m...
ZP_01034933  277 IVAAFDGDeiDINDest---adfIESYDALGLTKQSKptANTIVARmradtaPYDSKDLRNAIQLACDNAVLLAISInGE 353 Roseovarius sp....
YP_764646    286 GIAAMASKqvDGLSeadavqinaMKNFPHVAVYQVET--TQTVVARmhpdidQFKDKRVRQAMRYAIDRDKVIQTALlGA 363 Rhizobium legum...
NP_107690    275 QILALQGGqiDIINqmpvlagvaLLNDPSVDIISLKSvaHQQLHLRcd--sdPFKDPRVRRAIALSIDRDKLVAGLMkGR 352 Mesorhizobium l...
NP_103659    272 QVLALQAGqlDVIPsttr-lelaIEGNPNFKLLSVQAssHDPAHLRtd--qaPFTDKRVRRALALTIDREAVVKGLLkGR 348 Mesorhizobium l...
ZP_02884706  277 QLLALQGHqaDVMGtftvqggaaILNNPDYKAVGVKSsaHRQIHMRnd--npLFKDKRVRQALALSLDRDVLVRGLFkGR 354 Burkholderia gr...
YP_001235197 271 QVLALQGGqvDVIQqivvqgaqgLLHDPSVKILNIRSsnHREVHMRcd--kpPFTDKRVRQAVALTLNRPGIVHALFgGL 348 Acidiphilium cr...
ZP_02191729  291 QVAAIASGqvDGIYevdvsqldvYDALPGVKIYEAAT--AQTAIGRmkvtekPFDNIKVRKAVQLCMDTDAILKIAYrGR 368 alpha proteobac...
NP_108411    279 TLNAFESGeiDLDFetp---adfIDPLDKMGLVKSEVatATTLVARtnithkPYDDQRVRNALQMAVDNNAVMQLGYaGL 355 Mesorhizobium l...
NP_105385    273 MLSAFESGeiDTDHeta---sdaVSQTDKMGLKNSEIatGSTIVARfnignaPYDDVKVRRAAQLAVDNAAVLALGLgGR 349 Mesorhizobium l...
CAB01955     337 GTVGNDTPMIKGYPLfdddIEQRVFDPDRAKFHFKKSGHd----gSILLRTSDvafpgaVDAAQLFQASAAKCGIDVELK 412 Sinorhizobium m...
ZP_01034933  354 GVPAENHHVAPFHPEya-eLPAIAADPAKAIEMARAAGHgd---tEIDIISIDgd--wrTTTTDAIGAQLRQAGFNVKRT 427 Roseovarius sp....
YP_764646    364 GIPAEDHHVAPSHPEya-aLPKYPRDIEKAKKLLADAGYpd--gfEFDMVTRPdpi-weLNTAQVLAEQFKDIGVKINIK 439 Rhizobium legum...
NP_107690    353 ASAGNDSPFAPAYPStdtsVPQRKQDIAQAKQLMEAAGAgk--gfKVTLTTERyl--eiPEYAQLIQNWVKEIGIELELN 428 Mesorhizobium l...
NP_103659    349 AVVGNDTPFAPIFPSadpsVPQRKQDIAEAKRLLGEAGVpn--gfEVTLTTERay--diPDYAVIIQNFARKAGIDIKLN 424 Mesorhizobium l...
ZP_02884706  355 AQLGNDSPFAPVFPSsdagVPQRRIDVAKAKQLLAQAGVpn--gfDVTLTTEKym--eiPDLAVVVQNAAKAIGVRINLK 430 Burkholderia gr...
YP_001235197 349 SDLGNDSPFAPIYPStntsVPQRHRQIARAKHLMAEAGLah--gaEVTLTTEQvq--eiPDYAVLIQNAAAEIGLKINLK 424 Acidiphilium cr...
ZP_02191729  369 GQAGEHHHVSAIHPEyf-kLPKPKYDPAAAKKLLAEAGYkdgitlKVDFGQTSgs--weLAAMQAFKEQCAPAGINLELS 445 alpha proteobac...
NP_108411    356 GTVGENHHVAPIHPEyy-pLPKKTRDAAAAKKLMADAGQad---fEHELITVEde--wqKNTGDAIAGQLRDAGIKVKRT 429 Mesorhizobium l...
NP_105385    350 GKPADNHHVGPMHPEya-dIGPAKRDVEEAKNLLAASAKpd---hEYELISVDve--wqKSTGDAISAQMREAGLKIKRT 423 Mesorhizobium l...
CAB01955     413 rePGDGYWSDVWnk------qpFSMSYWtgrpt----------qdqvYSIAYLs-----KAEWNDtrffREDFDKLIFAA 471 Sinorhizobium m...
ZP_01034933  428 viPGSSFWNDWTky-------pFSTTNWgprpl----------gvqvLALAYKs-----GEAWNEsghaNPEFDALLDEA 485 Roseovarius sp....
YP_764646    440 slPSAQYWEVWTta-------pFSLTAWghrpl----------aimtLSLAYRs-----NAAWNEsnysNADFDKLLTEA 497 Rhizobium legum...
NP_107690    429 ilDQGAYYGDAV----------FGKSNWldsvmgi-----tdyghrgVPNVYLaaplksDGTWNAahfkNKDYDTLANSY 493 Mesorhizobium l...
NP_103659    425 vlPQDAYYGSAT----------FGSSPWldsnlgitdfghrgtpdifLNATLKs-----SGAWNAahfnNPDYDALLIDY 489 Mesorhizobium l...
ZP_02884706  431 veSQSLYYGAGTpgksdwldspLGITDYghrgv----------pnvfLNAPLTs-----GGTWNAahfqNPQYDQLVAQF 495 Burkholderia gr...
YP_001235197 425 ieTSAAYYGKAT----------FGNSDWldstmgi-----tdyghrgVPNVFLtaplesGGSWNAahfnNKTYDKLVADY 489 Acidiphilium cr...
ZP_02191729  446 pvPSATYWGIWTst-------pFGLTAWthrpl----------gvmvLNLAYRs-----GVPWNEssyaNPAFDKALDEA 503 alpha proteobac...
NP_108411    430 vlPGSTFWNDWTky-------pYSMTIWymrpl----------gvqvLALGYRs-----GEAWNEtayaNPDFDAKLKQA 487 Mesorhizobium l...
NP_105385    424 vlPAATFWNDWSky-------pFSCTEWlgrsl----------gvqvLALAYKs-----GAAWNEsayaSKEFDDLLDKA 481 Mesorhizobium l...
CAB01955     472 RgelDEAKRKVLYREAAMILRDeGGVIAPMFNnyIDATSD-KVGGW 516 Sinorhizobium meliloti
ZP_01034933  486 LgifDADKRREYSAKLQAMLQDsGAVIQPFWRnqALHHTD-KVKGV 530 Roseovarius sp. 217
YP_764646    498 EgilDPKERSKVMAKIEAIMQDdGPIVQPFWRv-FSTVMDkKVKGF 542 Rhizobium leguminosarum bv. viciae 3841
NP_107690    494 IaalDLEAQKADAGKIQKLLLEeTPVIFGYFYdyLTATAK-GVAGV 538 Mesorhizobium loti MAFF303099
NP_103659    490 GkarDLQAQRVAAGKIQNLLLDeTPLIISYFSq-YSRIVSaKVEGV 534 Mesorhizobium loti MAFF303099
ZP_02884706  496 VaavDLASQKKISGQIQTLLLDeTPIIIPFFYdqLIAMRK-GVNGV 540 Burkholderia graminis C4D1M
YP_001235197 490 IatvDLTRQREYSGRIERLLLDeTPIIFAYFYnyLAATKK-TVSGV 534 Acidiphilium cryptum JF-5
ZP_02191729  504 SailDVSKRKAAMEKVEKILQDdAIMVQPIWRsvFSAATD-KVKGF 548 alpha proteobacterium BAL199
NP_108411    488 LslaDPAKRKEVMKDVEQILQDsGVIIQPFWQk-LYCHMNkKVKNY 532 Mesorhizobium loti MAFF303099
NP_105385    482 LatpDAKARKEIMAGIEKNLRDsGIIIQPYWRs-VYRTYRkGVEGC 526 Mesorhizobium loti MAFF303099
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