Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_2

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cd08498: PBP2_NikA_DppA_OppA_like_2 
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: 173863
View PSSM: cd08498
Aligned: 71 rows
Threshold Bit Score: 483.603
Threshold Setting Gi: 193782669
Created: 26-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:
NP_769517     27 TLRYANqgdlksLDPYTlnestTHAHLgHVYQGLTARDk---dLKIIPALAESWETpeptRWRFHLRKgVKFHNGDPFTA 103 Bradyrhizobium ...
YP_002546802  52 VLSIAQgndilsLDPADhgnnsTESALvNIYDYLVTKDfsgetLVFTPNLAKSWSTsdqvRWVLNLRDdVRWHDGSKFTA 131 Agrobacterium r...
YP_001918926  51 RLTIGMgtdmvtFDIHDhnntsTEAVH-INIFDYLFRQe---dGEIQSELVSKHEIiddeTWKFKLKEgVKFHNGDELTS 126 Natranaerobius ...
YP_001525829  28 TLTIGVrsgpasMDPHFtstgvQAEAAkHVFDTLVKSGd---nLQLEPGLAESWTAvddtTWEFKLRKgVKFHDGSDFTA 104 Azorhizobium ca...
ZP_02187673   27 TLTVGVrggpesMDPHYsalgvHADAMkHVFDTLVWSGd---dLQIEPGLAESWKPlddtTWEFKLRKgVKFHDGSNFTA 103 alpha proteobac...
YP_177155     48 TLTIAQgsdmvsFDVHDhsntsTEAIHiNMFSYLVKNDve--gEGIVPDLATDWELvddeTWQFTLRDdAVFHNGDPVTA 125 Bacillus clausi...
NP_241213     40 TLTIAIgtdivsFDIHDhnntsTEAVHdNMFNYLFKRDe---nNVIQPELVETFESiddrTVEMTLKEgVTFHNGDPLTS 116 Bacillus halodu...
YP_175101     42 QLTIANpadittFDPHNnsvitTSAVLvNVYSKLLKRDe---aGEIIPELAESWDTiddvTWEFQLRDdVTFHNGDPFTA 118 Bacillus clausi...
NP_437149     34 ELRIATsyklmtLDPQYanlneNTSLLsHIYERLVYQDd---nLELKPGLATSWRPlsdtQWAFKLRDkVRFHDGSAFDA 110 Sinorhizobium m...
ZP_02169357   69 TLVIAMgtdmvsWDVHDhgntsTEAVHvNVFDYMFKRAeg--tMEIEPHLVEEYETleddLWEFKLREdVYFHNGDQLTA 146 Bacillus seleni...
NP_769517    104 DDVVFSADRVRKkgsnmqt----rlapdvkVVKVDDYTVDFVLpspnPILHNAWdvwyimdkkwaeennvvdptpvaatt 179 Bradyrhizobium ...
YP_002546802 132 NDVKFTVERTQGdpklksan---kfssvkaVKVIDDYTLQIETkypnPLLLHSFvgngagllpklaf--------eaagd 200 Agrobacterium r...
YP_001918926 127 KDVQFTFHRVIEdssltehs---nynqiseVEVINDYEFYIHTedpePALLNRIsrmgsgilpkdy---------ieeeg 194 Natranaerobius ...
YP_001525829 105 EDVKFSIERIPNvtgpnptt--vyvrrvktVEIVDPLTIRIKTdgpaPTLPNDFvrlfvvshtaakdfs----tkdtagd 178 Azorhizobium ca...
ZP_02187673  104 EDVKFSIERIPVvtgpttll--iyvrrvkeVVIIDPHTVHLKTdgpaATLPNDFvrlfivshkaaadfs----tketaag 177 alpha proteobac...
YP_177155    126 EDVKFTLERVAKdntlqehe---nyrqineVEVIDDHTFLIHTngpqPVMLNRLsrlgsgilpkdy---------ieeng 193 Bacillus clausi...
NP_241213    117 EDVKFTLERVATddtlqeyp---nykqikeVEIKDELTFRVIThepePSLFHRLsrlgsgilpkty---------ieeeg 184 Bacillus halodu...
YP_175101    119 EDVKFSLERVANdttlqqya---tfsqienVDVVDDHTIQITTaepdPQLLSRLstpaasmlpkdy---------feevg 186 Bacillus clausi...
NP_437149    111 DDVVYTIERIRDflkppsggfrsyvsgiksVSAPDPLTVLIETdgavPNLPLFFsslfvmnrpskg---------fette 181 Sinorhizobium m...
ZP_02169357  147 EDVKFTFDRVLGddslseha---rftqlgeIEVIDEFTLQFNTdgpqPTILNRLaqtgagilpkdy---------ieeng 214 Bacillus seleni...
NP_769517    180 psyaslhENGTGPFIIESHQPgVKTVFKANPNYWgk-vEGNLKEIIFTPIssdATRVAALLSGEVDVIEpvPIQDisrvd 258 Bradyrhizobium ...
YP_002546802 201 kdvffrnPVGTGPYRFKEWRKaDRLFLEKNADWWg--gQPKWDSVVVRAIpetATRVSEFITGGVDIAVniPPEDierik 278 Agrobacterium r...
YP_001918926 195 wdhfldsPIGSGPYEFVEWERdNRVVLNPFEDYYgd-yDSPWEEVVYRVIpedSTRVSELLTGGVDLAVnvPPTDwdrvd 273 Natranaerobius ...
YP_001525829 179 gfnsgkaTIGTGPYKFVSWTPkEELVLTRFDGYWg--gKEPWEKVVRKEIpndAARVAQLKAGQLDLISrvPPADvptle 256 Azorhizobium ca...
ZP_02187673  178 gfnsgkaAIGTGPYKFVSWEPkGDLVLERFDGYWr--gKGPWAKVVRKEMpndSSRLAALKAGQVDLINyvSSADwqalk 255 alpha proteobac...
YP_177155    194 wdhflqePVGSGPYQFVEWVRdDRVVLERFDDYFgg-dVAVWDQLVFRSIpesSTRVGEVIAGGVDIAMniAPIDwnrvn 272 Bacillus clausi...
NP_241213    185 wdhflanPVGTGPYQFKEWVRdSKIVLTPYENYFeg-aVDEWDEVVFRVIpenSTRVAELLTGGADIAVniPSADwerve 263 Bacillus halodu...
YP_175101    187 adeffkaPVGTGPFQFESWQQdEAVVLSKYEGYFe--gEPNWETVRFSVVpedSTRVSELLTGGVDIAFniPTADmerid 264 Bacillus clausi...
NP_437149    182 nlnaghpPNGTGPYRFESWSSgESLRLARNDDYWg--gKPAWSKVTFRVIenpAARVAALSTGEVDVAHaiPARDvasl- 258 Sinorhizobium m...
ZP_02169357  215 mdhflenPVGTGPYEYVEWVRdDRVVLSKYDNYFlgddFTEWDEVVFRAIpesSTRVGELLTGGAHVVTdiPPNEwprvd 294 Bacillus seleni...
NP_769517    259 -sspnAQVLKGPElRTIFIGFDqmrdell----ysnikgkNPFKDIKVREAFYKAIDIELIKTRVMrGLATPsalmiape 333 Bradyrhizobium ...
YP_002546802 279 -ankgTRVISFDIaRNLALHVRtg--------------ekWVTHDPRVREAIDLAIDRNTIAQQVVnGYGSPtrgffpkk 343 Agrobacterium r...
YP_001918926 274 -dnqgTLISTGDSnRVMLLILNhe--------------egRPTEEQKVREAIDYAIDNEALTESILdGQGTPvrtrvtpg 338 Natranaerobius ...
YP_001525829 257 -kdakLKVDKADSvYVFLVEFDfrdkpalvtakdgsplpkNPFLDPKVREAFDLAIDREALAEIAMeGLGKPasqlvtdt 335 Azorhizobium ca...
ZP_02187673  256 -rdpkTDTFLADSvYVMNLQLDqrestpkvydldgkplakNPLRDPKVREALDLAIDRPTMVEVVLeGLGTPnnqlmpkg 334 alpha proteobac...
YP_177155    273 -enegTSIVEGQTnRTMMLVPNhr--------------eeYPTSDPLVREAIDLAIDNQALLDNLMgGSGTPtltrvnpg 337 Bacillus clausi...
NP_241213    264 -enegTSMKTETSnRTIMLILRat--------------egYPTADVRVRQALDLAIDNKAITENVLrGGGIPtktrvapg 328 Bacillus halodu...
YP_175101    265 -nndgTHMALEPIqRVIQIWLSne--------------egETTADPAVREAIDLAIDNQVIIDEILqGSATAtrthitpg 329 Bacillus clausi...
NP_437149    259 -kqrgAKIASVGAaRVNFVQFDvardtlpgvtdksgepiaNPFKNPLVRRALTLATDRGILVDKILaGYGTAaaqvfpng 337 Sinorhizobium m...
ZP_02169357  295 dnegtRHVTAESNrTMLIIARQte---------------gSPGSDPRVLEAIEYAIDNEAITEQVMsGSAVPtrtrvlpg 359 Bacillus seleni...
NP_769517    334 lf-ilskeftrpkFDPDGAKKLLTEAGYpDGFEVTMDCPNDryvnDAAICQAVVGMLARIGVKINLLaqPKAQYFAKVLK 412 Bradyrhizobium ...
YP_002546802 344 ipgsnpelsanlpYDPEKARTLLREAGK-EGAAIKLSTPSGryvkDREISETVVGYLEDAGFRPQLEvlDWTIYNSRLTA 422 Agrobacterium r...
YP_001918926 339 ntgyneelyddyrYDPDYSRELLEEAGYsDGVELKFHAPQGrylmDSDVSEMITGMLAEVGINADLNllEFSQFADKYLG 418 Natranaerobius ...
YP_001525829 336 if-gfnkalkvtkADPKKAKQLLAEAGYpNGFKVALTFTTDrlqsDGAVGTSIVQMLAAAGIDAQANgqPSTVFFPARTR 414 Azorhizobium ca...
ZP_02187673  335 ff-gwsakvparsPDPRRGKALLAEAGYpNGFMMDLYCTSDrlpgDGAICQGLGQMFAQIGVKTNVNaiSRSVYFPAQAK 413 alpha proteobac...
YP_177155    338 nfganealhgeyrYDPDRAKELLEEAGYgDGLELTLHSPDGrylqDRETTEVIAGMLSEIGIDVKIDfmEWSAYVDLRDA 417 Bacillus clausi...
NP_241213    329 nfgaeeslyntydYDVEKAKQLLKEAGYpDGFEMTLHSPHGrylqDAEVAEMIAGMLQAINVEVRLEfmEWSNFVEMRQA 408 Bacillus halodu...
YP_175101    330 nfgadpslydtyeYDPERAKEILADAGYeDGVTINMSVNNY----YTEMAEVVGGMLADVGITANIEliEQSQFANRLFN 405 Bacillus clausi...
NP_437149    338 lp-gtsanllpeaPNYDEAKMLLAKAGFpDGFNLVLAGPAGrypgDAESLQAVAQSWARIGVNAQPAaaPFSVFNTKRAA 416 Sinorhizobium m...
ZP_02169357  360 nvganedlfdtflYDPDRSRELLAEAGYeDGLELTLQSPQGrylmDSDIAEVIAGMVSEVGIDLNVEflEWSQFIEHYQN 439 Bacillus seleni...
NP_769517    413 qggyqtSFYMLGWTpstmdshnVLFDIMgcrddakssrgeanlggYCNKEFDAITDKVlvetDTAKRNQLIKQAYEIGNK 492 Bradyrhizobium ...
YP_002546802 423 dg--fgELYLWGMGsytd-gssLFQDDFkrh------------ydWTNAEFNSLREKArnpgSEDARLAILRRAQEIVAD 487 Agrobacterium r...
YP_001918926 419 ne--neDLMFLGLSn------sMFDAAHalrnfhse--qntertyYENERVDELLEKAesnmDFEERKEQYQEVQEIVAE 488 Natranaerobius ...
YP_001525829 415 gd---yGLSMWGWGtltgeanyTLAGLMhtntpetk-lggfnvrgYSNPALDKLIEQAavemDVPKRRTQLEEAAALVAK 490 Azorhizobium ca...
ZP_02187673  414 ke---ySIFMNGWGtltgeasyTLGSMAhspnaelk-lgafnrieYSNPKVDELLQAAgrelDAPKRKALYEQAMDLIMA 489 alpha proteobac...
YP_177155    418 he--qkDLYLIGLTgsl---wdAAHQLRhhtsmv-----aedhigYSNEEFDQIYLEAevnmDEAEREQQYIDLQTMADE 487 Bacillus clausi...
NP_241213    409 ge--nkDAYLIGLGn------sMFDGAYsvdwhrsd--rfvgetdYKNEEIDALLEASavnmDEEERAKQIQEIQRIAAE 478 Bacillus halodu...
YP_175101    406 ge--leEAIFVGWGn------dMFDASVldffkk------egvapYTNPEIEQLLEDAaynmDEEERADQYQQVQQQLAE 471 Bacillus clausi...
NP_437149    417 gd---yGVWYGGTSgea--vdiILHSLLaspdperg-tgalnfgkYRNEAFDAMLAGAesiaVGPERNAALAQATELVMA 490 Sinorhizobium m...
ZP_02169357  440 nt--neDLMLLGLAtslydaaqALDHYYsdspln------egrmdWVNEEFDELFFAAetnmNPEERVEQYHRAQELVAE 511 Bacillus seleni...
NP_769517    493 dWSYIPLHQQalAWGVSK-KVNLPQRAD 519 Bradyrhizobium japonicum USDA 110
YP_002546802 488 qRVRIGLIYPqsIYGVND-RIKFDGRFD 514 Agrobacterium radiobacter K84
YP_001918926 489 eLPYVYLYQQkdSYGINN-RIDFEPRLD 515 Natranaerobius thermophilus JW/NM-WN-LF
YP_001525829 491 dRPTLPIASIvsAWAMQKaKVTFTPRVD 518 Azorhizobium caulinodans ORS 571
ZP_02187673  490 dRAYISIVTLqtVWASDKgKLKMTPRTD 517 alpha proteobacterium BAL199
YP_177155    488 eLINIMLFQLdsFYAVND-RIQFEPRLD 514 Bacillus clausii KSM-K16
NP_241213    479 eVPHIMLHQEtlHYGVSD-RIAFVPSMD 505 Bacillus halodurans C-125
YP_175101    472 dRGAVYLFQLqgRYGVSD-RLDYKPRLD 498 Bacillus clausii KSM-K16
NP_437149    491 dQPIIPLYHFhhIVGYGS-RIGSYLLHP 517 Sinorhizobium meliloti 1021
ZP_02169357  512 gRPHIYLHSInmNFGVSD-MIDYEPRHD 538 Bacillus selenitireducens MLS10
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