Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_19

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cd08518: PBP2_NikA_DppA_OppA_like_19 
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: 173883
View PSSM: cd08518
Aligned: 44 rows
Threshold Bit Score: 459.746
Threshold Setting Gi: 226357570
Created: 6-Feb-2010
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:
P06109        50 ESVVIGVasepdtLSPLLg-yGKDGNsk--iFDGLLARDtdlELKPAlAAALPKVTDDgrTITFTLREgVNFSDGEPLTA 126 Streptomyces li...
YP_001029612  33 NTLVYAGegv-dsINPIF---DTHGEltnvvFSGLMTYDannQPIVD-LAESYTYDDKnmTYTFKLKKgVTWHDGEPFTA 107 Methanocorpuscu...
YP_001253874  43 KTVVYGAefedekLNPVLa--PAYANdl--iFRGLMRFDkdnKPQCD-IAESYKKSTDglTYDFKIKKgVKFHDGKELKA 117 Clostridium bot...
YP_001087332  38 KVLVYGSndy-tsINPALyehGEINSl---iFNGLTAHDennKVVPC-LAKDWKFDEAtnTYTFNLRDdVKWHDGEKFTA 112 Clostridium dif...
YP_002576017  21 DTIIIAVeneperVNPLFs--EDHDVaialvFSGLTRFDenmSLAPD-LASSWKVSKDglVYEFTLRDdVLWHDGTKFSA 97  Campylobacter l...
YP_001467566  21 NAVVVAIeeqtprINPLYd--EDHDPtlslvFSGLTSHDensHVVPE-LAKSWQVSDDglEYVFELRDdAFWHDGVKFSA 97  Campylobacter c...
ZP_01809418   41 DTLIVAVeneisrINPAYs--EDHDAvinlvFSGLTRFDehmSLKPD-LAASWNVSKDglSYDIFLREdVLWHDGVKFSA 117 Campylobacter j...
YP_892780     22 DTIVIGIenetsrINPLFd--EDHDTaldfvFSGLTKFTpdmKIKPD-LAKSWKVSEDglVWTFYLRDdALWHDGEKFSA 98  Campylobacter f...
YP_001698376  29 NELVFASesefagLNPLL---EETNLda-flFRGLMRFDehnVPVFD-MAKSIQISDDqmTYTIVINDhVLFHDGQALTV 103 Lysinibacillus ...
ZP_01966215   32 TTLVYGSgdy-trINPAM---DEHGEiniliFNGLTAHDgdnQVVPG-LAESWKFDDAtnTYTFHMAEdAKWQDGEPVTA 106 Ruminococcus ob...
P06109       127 GDVYTYRTVLDEktnntar---seldavrERSARa--DGTVVFTLKYPYAPFAARTvLPIVPEhvagkqdpntgdFNTEP 201 Streptomyces li...
YP_001029612 108 DDVVFTYNTMLTdaavsssvrsdyediatVTAPD---DYTVVITMDKYNAAMLDYFaLGILPKhllegkdiatdsFNQNP 184 Methanocorpuscu...
YP_001253874 118 EDVVFTIKSIQDpkvntem----kpefeeVKDIKaegDYNVKVTLAKPFPALLDKLtIGIVPKhalegkdlnnaeFNQKP 193 Clostridium bot...
YP_001087332 113 NDVKFTIETIMNpdnasei----asnyedITKIDvvnDNTIKITLKAPNTAMLDYLtVGVLPKhalegkdiatdeFNQKP 188 Clostridium dif...
YP_002576017  98 KDVEFSINALKDeklnspsk-vnfdavkeVKIID---DYHLSITLSKPFPAFLDALsVGILPKhllenenlnttkFNQNP 173 Campylobacter l...
YP_001467566  98 KDVKFTIEAAQDkklnapa----isnyevVKSVEilgDYKVKITLKEPFPPFLDALsFGVLPEhilkgkdiatdkFNDAP 173 Campylobacter c...
ZP_01809418  118 DDVKFSLEAFKNpknnssi----yvnfedIKSIEilnPYHLKITLSKPFPAFLDALsIGMLPKhllsdkdlntasFNQNP 193 Campylobacter j...
YP_892780     99 EDVKFTIEQALNdklnapa----kasfeeVQSVEvinKYELKIMLKSPFPPLLDALsIGVLPKhildgkdinsdkFNQNP 174 Campylobacter f...
YP_001698376 104 DDIIFTIESILDdangsylk-sdfihvtgMKKID---DSTMTIQLDEPFTPMLDKLtVPILPKhafegqemrtasFNQQP 179 Lysinibacillus ...
ZP_01966215  107 DDVKFTIEAIMDpengsena-pnyedveeINVVD---DHTVEFKLEDKNVAFLDYMtMAVLPKhllegedmqtsdFFRNP 182 Ruminococcus ob...
P06109       202 VGTGPYVLTGWSKg-EKLGFRANPHYWg--dKPAVKSFTMAVtaddnvRATRLRSGDLDGAVLppnlaat-fekddgrRT 277 Streptomyces li...
YP_001029612 185 IGTGKYKLSDWDTagGMIILERNTDYYg--nVPNIERVIYKTvgvestKATMLMTGEADLAWLnsnyakq-frgksgyTN 261 Methanocorpuscu...
YP_001253874 194 IGAGPFKFVKWEKg-NNITLSKFEDYYgkdkTGNVEKFIFKFipdynvRAMQLETGEIDLAYVepsqvak-leklekiKI 271 Clostridium bot...
YP_001087332 189 IGTGPFKLEKWDKg-QSITLVKNSDYFv--kEPGLDKVVFKIvpddkaKAMQLKSGELDLAQItpkdmsnfekdeknfKV 265 Clostridium dif...
YP_002576017 174 IGTGSYKLKQWKQg-QYMLLEANENYHl--aKVKTPKLILKHikdpsiSAIELKNGSIDVALVdfslasn-fkddknfKI 249 Campylobacter l...
YP_001467566 174 IGTGAYKLVKWKKd-ESLEFVANDKFYk--gEPKIKRLFLKIvgdenlRLVGLKSGEIDVALIsptgvnf-ikddkklSL 249 Campylobacter c...
ZP_01809418  194 IGTGPYKFVKWKKg-EYVEFKANENFYl--tKVKTPRLIIKHifdpsaASVELKNGKIDAALIdvsllni-fkkdenfKI 269 Campylobacter j...
YP_892780    175 IGTGPFKFKKWQKg-SYISFEANKDFYr--gKPKADKVILKIvpdyniRTYEIKRGDLDVALIesnlvke-lqndkniKI 250 Campylobacter f...
YP_001698376 180 IGAGPYRFEQWDKg-TSLTLKAFPTFYg--tKASIEQVIFKFipdsnvRALQLKSGEVDIALLdpnqvee-lskverlKM 255 Lysinibacillus ...
ZP_01966215  183 VGTGPYKIESWDEg-QAITLAKNDDYFk--gEPSIDKIVFKIvpddnaKALQLKSGELDLALLtpkdaaa-fagddayTC 258 Ruminococcus ob...
P06109       278 YRARSydFRAVTLPsagq---vtgDRAIRRALDAAVDRQAMVDKILdGAGRPAYgplpVDDPWyerg--ierPRDLAAAG 352 Streptomyces li...
YP_001029612 262 YDFQTadYRGAAMDfrtd--fwkkNGDSVGVLNYAIDKDAIVNSVLdGRGIVAFsp-mQLNSYggdtaadiySYNLTKFA 338 Methanocorpuscu...
YP_001253874 272 YNENTadYRCFMFNmrke---lwkDVNVRKAFNYAVDRKGMVDGILkGFGVEAYsp-lQKNKFnnan-vekySYNLEKAN 346 Clostridium bot...
YP_001087332 266 NIMKTadYRGILYNfnskffkdkkAKGLPNALSYAIDRKAIVDSVLlGHGVPAYsp-lQMGPYnnpd-iekfEYNPEKAK 343 Clostridium dif...
YP_002576017 250 LIEPSadYRALMFNldne---flkDKNVRLALNHAIDKQAIINSLLhSFGKVASh--pLEKSWanpkefasyTYDVKKAN 324 Campylobacter l...
YP_001467566 250 LKFKSadYRALMFNfndp---lfqDKNVRIALNYAVNKDEIVKKLFhGYASVANn--pIEKSFands-efkfSYDPQKAR 323 Campylobacter c...
ZP_01809418  270 LRERSadYRALMFNlenk---flkDIQIRKALNYAVDKQSIVKNLLhDYGFVANh--pLERSWadskafktyEYNPKKAQ 344 Campylobacter j...
YP_892780    251 MKLDSadYRALMFNfdne---ilkSLAVRQAINYAIDRELIATKILhGYGFSANn--pIQKSWandknakiyEYNIEKAK 325 Campylobacter f...
YP_001698376 256 YEVESadYRGVLFNmkyp---iwkDVSLRKAISYATDRAGIVKGILhGYGTEAYsp-lQQHNFvnek-iehyTYDVKKAN 330 Lysinibacillus ...
ZP_01966215  259 YDMKTadYRGIMFNfgne--ywqkNRDLIPAVCYGLDRQAIIDAVIlGQGMPAYgp-lQRNTYnced-vehyDYNPEKSK 334 Ruminococcus ob...
P06109       353 RILDEAGWkpgsggirardgqRASFTLYYPsgdkvRQDHALAYASDAKKAGIEVKVEgatWEVIEPRMKTdAVLADLGSv 432 Streptomyces li...
YP_001029612 339 EEMEKLGWvkgsdgiyerngqKFHFTIQTRdyeeeRVDIANLMSQMLETAGVDMEVVl--VTKFDWNSGYnGFLAGYATe 416 Methanocorpuscu...
YP_001253874 347 ELLDKAGWkkgqdgirekdgkKFEFTLTAPstdevRVKIANYLASQFKKIGVTVKVAaldWNAIKIDECE-AFVLGWGSp 425 Clostridium bot...
YP_001087332 344 QEIEKLGWklgsdgiyekegtKLAFEITAGesdqvRVDMAKICAQQLKEIGVDAKAVv--VTETDWANQD-AHLIGWGSp 420 Clostridium dif...
YP_002576017 325 ELLAKAGFvknkngilekdgkEFSFDMYAMsedplRVALVNILQSEFLKLGIKAKAIakpSGSFDYTKED-SFLVGWGSp 403 Campylobacter l...
YP_001467566 324 ELLEKSGFkknkagffekdgkELAFDIYAFnndilRVNLAKILSSEFEKFGVRAKAYakpKTAFSISKVD-SFVIGWGSs 402 Campylobacter c...
ZP_01809418  345 DLILALGFkkndegifekdgkILEFEIWAMsndplRVSLAGILQSEFRKIGVVSKVVakpAGSFDYSKVD-SFLIGWGSp 423 Campylobacter j...
YP_892780    326 EILANDGWelknkv-lqkngkRLEFDIYAFngdpfRVTLANIIQSELSKIGIKARAIaknHGAFEIDKVD-SFIIGWGSp 403 Campylobacter f...
YP_001698376 331 KLLEQAGWqladdgfrykdgqKLTFTITAPitdtvRVNMANYVAEGYKAVGADVKVAaldWSNIVIEETE-AFMVGWGSp 409 Lysinibacillus ...
ZP_01966215  335 EILEAAGCemgddgfyyrdgeKVGFVISVSagdqvRIDMAQIAAQELREIGMDVSVEi--PAQTDWAGQM-AFLIGWGSp 411 Ruminococcus ob...
P06109       433 gdpdfGLYTLLHstl----agdGFNNmahYANPAVDEALDAGRRsqDPKVRAAAYREIQKALVADPGYTFLTHIDHLYVL 508 Streptomyces li...
YP_001029612 417 yd-pdMMYAQFTt--------nGSSNtmkYSNAEVDEILTQARHeaNPSVRKQLYGEFEQVFAETPGVLLTAYLEGNYVG 487 Methanocorpuscu...
YP_001253874 426 ydaddHTYKLFHssq-----ikNGNNfgaYSNPKVDKLLEEGRTteDEEKRKEIYGKLQEELANDPPYNFEIYVNAIYAV 500 Clostridium bot...
YP_001087332 421 fdpddHTYKVFGtd-------kGANYs-aYSNPTIDKILQKAREteDKDEKLKLYKQFQVEMTKDMPYTFIAYIDAIYVG 492 Clostridium dif...
YP_002576017 404 ydpdfHTFRVFAssqdsalnssGWNFg-hYKNAKVDEALTKARNslDVNERKKHYKEFIDALQDDPAFLFIAYIDYPLVY 482 Campylobacter l...
YP_001467566 403 fdpdfHTYRIFGgfadidvnenGWNFs-hYKDANVDLALKNARYtkDVELRKKYYKEFLKALFENPPYIFIAYLDYPLVF 481 Campylobacter c...
ZP_01809418  424 ldpdfHTFRVFEssqdsalndeGWNFg-hYHDKKVDIALQKARNtsNLEERKKYYKDFIDALYENPPFIFLAYLDFALVY 502 Campylobacter j...
YP_892780    404 ldpdvQTYRVFSskmdaaknenGWNYn-hYSDKTVDETLLKARTtdKTEERKLWYSKFINALHEDPPFAFLVYLQYPLAY 482 Campylobacter f...
YP_001698376 410 ydadhHTYSLFHsgess-ltsaGYNYg-sYANAKVDALLEEGRTtvDPEQRKKVYMALQEELAQDPPFAYFAYVDAVYGI 487 Lysinibacillus ...
ZP_01966215  412 fdaddHTYKVFGtdk-----gaNYSS---YSNEEVDKYLTEARQsdDPEVRKEAYANFQKALAEDPAYAMICYIDANYVA 483 Ruminococcus ob...
P06109       509 ADRWDGL 515 Streptomyces lividans
YP_001029612 488 IDGLSGL 494 Methanocorpusculum labreanum Z
YP_001253874 501 NKKVTGI 507 Clostridium botulinum A str. ATCC 3502
YP_001087332 493 KPNIKGL 499 Clostridium difficile 630
YP_002576017 483 AKNIQGI 489 Campylobacter lari RM2100
YP_001467566 482 NNKISGI 488 Campylobacter concisus 13826
ZP_01809418  503 NKDLKGI 509 Campylobacter jejuni subsp. jejuni CG8486
YP_892780    483 SDKISGI 489 Campylobacter fetus subsp. fetus 82-40
YP_001698376 488 DKQINGV 494 Lysinibacillus sphaericus C3-41
ZP_01966215  484 DSNIKGI 490 Ruminococcus obeum ATCC 29174
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