Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_11

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cd08516: PBP2_NikA_DppA_OppA_like_11 
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: 173881
View PSSM: cd08516
Aligned: 25 rows
Threshold Bit Score: 551.855
Threshold Setting Gi: 167771088
Created: 1-Jun-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:
NP_107608     30 TLHMAWSqdatgLDPHKqtafsSLRLLelIYEPLVRVDasLQIIPAIATSWAFSkdgkELTFKLDPkAKFQDGTAVTSAD 109 Mesorhizobium l...
ZP_02443141   44 EILFGVPadvssLDPQTqndsySEEVVkmVYNTLYVFDenNTPVPSLAESYEVSednlSWTFHLRTdVKFHNGKTLTAKD 123 Anaerotruncus c...
NP_604256     32 SIRTVSTvdidsLNPYQvvssaSEQILlnVFEGLIMPGvdGTVVPALAESYEISedgrTYTFSIRKgVKFHNGNDMDIKD 111 Fusobacterium n...
ZP_03463707   62 SVVVGIQqdidsLDPHKataagTKEILfnIFEGLVKPDenGNLIKAVASDYKVSddglVYTFTIRDgIKFHNGNAVTVED 141 Bacteroides pec...
ZP_03755674   54 SVVVGIQqdidsLDPHKataagTKEILfnVFEGLVKPDenGNLICAVASDYSISddglVYTFTLRDgVKFHNGNDVTCED 133 Roseburia inuli...
YP_001557557  48 SVIVGITndldsLDPHKavaagTKEVLfnIFEGLVKPDkdGNLVPAVASDYKISedgmTYTFYLREgVKFHNGALVTVDD 127 Clostridium phy...
ZP_02431621   39 IVRMAVSsepdnLNPMKssatdTSAMMmnVYEGLLSFDknGSFIPALAESYEITddgmTYEFQLKEgIQFHSGDEFNAED 118 Clostridium sci...
EEO36950      33 EIKTTMSmdidsLNPYKmvssgTEEIMlnVFEGLLMPNskGELTPAIAESYKISedgrIYTFKIRKgIKFHNGNPLDVKD 112 Fusobacterium m...
ZP_04040705   24 ILRAGMQtdpvgLDPHTtnataSRNVLenIYDTLVMLDskGRIVPGLAQSWSVSadglTWTFRLRPgVTFHNGDPLKASD 103 Meiothermus rub...
YP_888629     34 NLIAAIAgepdqLDPQKtsayfSFEVLenVFDTLVEPDenLQMQPALAESWEVSpdqlTWTFHLRDgVRWHDGTPLTADD 113 Mycobacterium s...
NP_107608    110 VKASFERILDektgaaar-------anflsiasIDTPD-AATVVFHLsqPDVPILTAMsdvnaaivpas-----eikags 176 Mesorhizobium l...
ZP_02443141  124 VEASFNRALPedsgyitt-------smispiesVTAAD-DATVVIKTkePYGPMLSLLcnyntaimdsdfieqygrdlgt 195 Anaerotruncus c...
NP_604256    112 VEFSLNYMSGklgnnpte-------alfeniekIEILD-DSHIAIYLskPDSSFIYYMkeaivpde----------nkdh 173 Fusobacterium n...
ZP_03463707  142 VKYSLDRASGlldgnali-------talkkisaVNIVD-DRTVEVTLasADTEMIYNFtaaiipkpa--------dgtqa 205 Bacteroides pec...
ZP_03755674  134 VKYSLERAAGlldgtplv-------atlqtiqsVDILD-DKTVQVTVdtPNTELIYSFvtaiipag----------sged 195 Roseburia inuli...
YP_001557557 128 VIYSLKRATGlletsdpevrvesvfscvesinaITTEDgKQAVEVKLnqPNIELLSYFtisiipkd-----------yte 196 Clostridium phy...
ZP_02431621  119 VKYTYETLAGlngesplne------tlaselvaVETPD-DYSVQLKLnkVDAGFLSKCtisiqqdg-----------ytq 180 Clostridium sci...
EEO36950     113 VEFSLNRMAGkdgfppas-------alfneiekIKVVS-EDEIEIKLkkADSAFIYALikgivpde----------nand 174 Fusobacterium m...
ZP_04040705  104 VVFSINRIKDpatkspra-------ndfalvrsVTAPN-NNTVVITLsqPFSPLLAKLafstnaivsekv---akehnnd 172 Meiothermus rub...
YP_888629    114 VVYSYRRIIDeqltnvd---------kfsavtdVSAPD-PATVRIVVshPTPNLLTNLggfkgmaivqr----gnvesgq 179 Mycobacterium s...
NP_107608    177 igtkAVGSGPFKLDKWDPnAKEVLSANKDWAs------gATGVDGIEISVLPDEaaILAAMRTKqIDFALlndplvatlv 250 Mesorhizobium l...
ZP_02443141  196 taetVNGTGPYKVASWAKdEEVVIEANPDYFg------nKAQVGAIHYLVIPESssRIIALENGeVDMIHkvpseevarl 269 Anaerotruncus c...
NP_604256    174 lkdiAIGTGPYKIAEYQKeQKLVLSKNEEYWg------eKAKISTVTILISPNSetNFLKLLSReINFLTnidpkr---i 244 Fusobacterium n...
ZP_03463707  206 dagkPVGTGPFKFVSYTPqESIILTKNEDYWqn-----gLPYLDEVKFKIVSGTdtALLELKGGsIDMYPyltdsqaeel 280 Bacteroides pec...
ZP_03755674  196 aeanPVGTGPFSFVSYTPqEGIVLAKNENYWqe-----gLPYLDEVDFKIVGSAdtALLELQGGsIDIYAyltdsqa--n 268 Roseburia inuli...
YP_001557557 197 qatkPVGTGPFRFVSYSPlVSIVMEKNPDYYvk-----gVPYLDEVTFKISANTdaAFMELRAGtIDIFQqltyeqsnql 271 Clostridium phy...
ZP_02431621  181 dstnPNGTGPYKFKEYVQgQKLVLEKNENYKtie---trMPEIDTVEFKIMTDSnaVLMALKSGdLDIASvdarnf---s 254 Clostridium sci...
EEO36950     175 ldknPIGTGPFKVAQYDReQQIVLDRFNEYWg------eKTKLDRVTVLIVPNSetAFLKLLSGeINMLSrvdskr---v 245 Fusobacterium m...
ZP_04040705  173 lnkaVIGTGPFRFVEYIPqTRLVVRKWDKYWqkdnqgrpLPYLDGITYTFYPDPaaRSTALRAGaVDWIEyvtaadvrpl 252 Meiothermus rub...
YP_888629    180 iathPIGTGPFAFAGRKSgDSITLKANPHYWg------pEPRVSGVTFRFISEPatALSALQAGeIDWTDsvppqrvaql 253 Mycobacterium s...
NP_107608    251 pkeasLQLNRVPVlaYHVLQLNpsrkpmtELKVRQAISCAIDRQEVLDTASlGEGKVtgpltipal---atdptqlfcYK 327 Mesorhizobium l...
ZP_02443141  270 etlegITVLKQPGvgQRLFRFGcndeimsNTKVRQALNYAVDRDAIRKALFaDVSEEttgplapav----fgshdygpIK 345 Anaerotruncus c...
NP_604256    245 peldkYQILSSPSnlCLILSLNpkekpfdDIEVRKAINLAIDKNKVIQLAMnGKGTPiytnmspvm---skflwnapeEQ 321 Fusobacterium n...
ZP_03463707  281 kstydIEYAISDV--AQALFLNnaeapfdNEKVRQAVACALNKDEINQFVAgGKSAVinsamlptik--nyyvdtnsyNS 356 Bacteroides pec...
ZP_03755674  269 elkdsFNVISSPSnvVQALFLNndyeplsDVKVRQAICYALDKDMVNEFVAgGNGTLissamlptlkyyyedlndlygTS 348 Roseburia inuli...
YP_001557557 272 kdlynIEIGHMNL--VQALFLNhkaapfdNLKVRQALSYAIDRQMILDIVAgGNGTIigsnmfpgfg-kyydeslasyYT 348 Clostridium phy...
ZP_02431621  255 slgkdFTSVEGPQnmVQIFALNnsveplnKKEVRQAINYAVNKEEIIQTVMeGHGTQlesflspsmk--nyynddikgYD 332 Clostridium sci...
EEO36950     246 nelknFNNISAPQntVQIFALNnnvelfnDIRVRKAINMALDKDEIINSVMaGNGIKletnmspvm---kkycienlgEK 322 Fusobacterium m...
ZP_04040705  253 kadrnLVVVGGPSanFRALYFNttrepynNPKVRQAIAYAIDKKAIVDLALfGTGGIvargttipsg--ayaytnspyNT 330 Meiothermus rub...
YP_888629    254 rdddsLTLAVTPSndYWYLALNearapwnDVRVRQAIAYGIDRDAIATATSyRTAAInqlaipegn----pwftsydrYR 329 Mycobacterium s...
NP_107608    328 RDVEKAKKLMAEAGFadgFSATVIGAtgepptaAAEAQVIQSQLAEIGVKLDIKMmELNVYVDAWLKG---DFDMAIALN 404 Mesorhizobium l...
ZP_02443141  346 QDLEKAKALLAEAGYpngFDTKIVTTtqy-dkgSELAEMIAAQLAEIGVNATIEVlEWSVFRPMISGMtaeEFDAPLFIM 424 Anaerotruncus c...
NP_604256    322 ANPEKAKQILEEKKLl-pMEFTLKVPnss-kfyLDTAQSIREQLKDIGITVNLEMiEWATWLSDVYTNk--KYVASLAGL 397 Fusobacterium n...
ZP_03463707  357 YNVSRAKQLLAEAGYpngFDMTIKVPsny-tfhMETAQVVAEQLKAAGINAKIEGiEWSSWLSDVYANr--DYQATICAL 433 Bacteroides pec...
ZP_03755674  349 ANVEKAKELLTEAGYadgFDLAIAVPsvy-efhMQTAEVVVEQLKAVGINATIDAvEWNTWLEDVYTNr--EYQATISGI 425 Roseburia inuli...
YP_001557557 349 YDVEKAKQLLNEAGYpegFHFTITVPsny-qahVDTAQVIVEQLKKVGITAEIKLvEWASWISDVYQGr--NYESTIIGL 425 Clostridium phy...
ZP_02431621  333 TNIGKAKELLAEAGYptgFTMTLTVPsny-qthIDTAQILKSQLEKIGVTVEIQLvEWAQWLENVYNNa--QYESTVIGH 409 Clostridium sci...
EEO36950     323 QNIDEAKKILEEVGKn-nFTFTIKVPsny-pmhVNTAQIIAEQLKAIGLKAEIETiEWTTWLSDVYSGr--KYEATIVGL 398 Fusobacterium m...
ZP_04040705  331 RDVAKAKQLLAEAGLpngFTMNLYVTsty-dflRTPADVIRDNLAEVGIRVNIQAeDWNVYLPKALRS---EFDVTLLGT 406 Meiothermus rub...
YP_888629    330 FDLDESKRLLDEAGAh-pENLDMLVTsey-petVTAAQIIADNLAPLGISVNIRTvDFATWLDEQNTG---NFDMLMMGW 404 Mycobacterium s...
NP_107608    405 gg---raDPYTMYNRYWtkagnl---qkvanYIDDTLDSQMQQGRaetDPAKRKAIFAEFEKHLAEm-SPWIWLYTSysY 477 Mesorhizobium l...
ZP_02443141  425 gagtsmaDADGGYRGLYtttpdgkndrnygfYSNAEVDEYIEQGMtetDPEKRKEIYAKAGQILYLddPAGIWLYDQlnV 504 Anaerotruncus c...
NP_604256    398 sg---kmEPDAILRRYTstypk-----nftnFNNARYDVLVEEAKrtsNEAKQVQNYKEAQKILSEe-QAAIFLMDPniI 468 Fusobacterium n...
ZP_03463707  434 ta---dlTPSSLLVRFTsgysk-----nfvnFSDAEYDKVYAEAQaslDDNVRKEKYAKLQQILAEk-EGSVFIQAAalL 504 Bacteroides pec...
ZP_03755674  426 tcs--dlTPGYLLNRFQtdskk-----nfvnFKSTEYDELWKATQatqDAAEKAADYKKLQTILADe-AASAFIQVPanT 497 Roseburia inuli...
YP_001557557 426 ds---nlSPSDIVKRYEstskn-----nflnYSNSQFDSLYPKAYasvKEEEKVDLYHQLQRILTEd-VASVYLQDPanL 496 Clostridium phy...
ZP_02431621  410 sg---klDPQDFLNRFTttyek-----nyfkYSNEEYDAKIAEAAsvtDETKRAEIYKECQQKLADd-AASVFIQDPsiN 480 Clostridium sci...
EEO36950     399 sgk--ldPYSILRRYTNdykn------nffnFSDEEYDMLIEKAKestNDEIIVANYKRAQEILREk-QAAIYIMDPelI 469 Fusobacterium m...
ZP_04040705  407 sg---qaDPDDYLFNTFhpssa----lnlskYKNDRVTQLLEQGRrvsSQSERQRIYTQVQELVLQd-SPMVFLFHSaqY 478 Meiothermus rub...
YP_888629    405 lg---niDPDDFYYAQHhsngt----snaqkFSDPEVDRLLDAGRvetDTAERKDVYARAATRIADe-VSYIYLYNPsvI 476 Mycobacterium s...
NP_107608    478 TAQQK-NIAGF 487 Mesorhizobium loti MAFF303099
ZP_02443141  505 FAYNSdKIDGL 515 Anaerotruncus colihominis DSM 17241
NP_604256    469 IATEK-GIEGF 478 Fusobacterium nucleatum subsp. nucleatum ATCC 25586
ZP_03463707  505 VAKNK-DLAGY 514 Bacteroides pectinophilus ATCC 43243
ZP_03755674  498 TAFNK-NLAGY 507 Roseburia inulinivorans DSM 16841
YP_001557557 497 VAVNK-KLAGY 506 Clostridium phytofermentans ISDg
ZP_02431621  481 YAVRN-TITGM 490 Clostridium scindens ATCC 35704
EEO36950     470 TSLDK-KIKGF 479 Fusobacterium mortiferum ATCC 9817
ZP_04040705  479 EAMNR-RVQGF 488 Meiothermus ruber DSM 1279
YP_888629    477 QAWSN-DLSGY 486 Mycobacterium smegmatis str. MC2 155
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