Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_15

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cd08492: PBP2_NikA_DppA_OppA_like_15 
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: 173857
View PSSM: cd08492
Aligned: 55 rows
Threshold Bit Score: 452.837
Threshold Setting Gi: 20092701
Created: 5-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_710626     47 GGSLTYALdve--------------------ptcFDLQVnqq------giTGDIErg-----vVDSLVTVDa-kGVFHPW 94  Frankia alni AC...
NP_125835     26 GGTPTQTQtqtgtgtsptettaalkhkvlvigytRDPDTldp------qkSTWVDitt--glvFATLINMGt-nGKIIPG 96  Pyrococcus abys...
YP_001433900  64 GRTRLVFFg------------------------nLEPASidv-----itmSGNVNerqvaaqiFETLVYMDq-sQQIYPG 113 Roseiflexus cas...
ZP_02189938    1 MGALALAVllpattpvvaet--svtimrtidtdrYDPHRst--------aRSTAEalf---mvGDTLVALDpdlKSVHPL 67  alpha proteobac...
YP_002772101  49 GGTITVAYase--------------------adtLDVHKsv-------gnDMGVTwn-----mGGSLVYKDpvtKEFKPN 96  Brevibacillus b...
YP_002773614  39 GNTLVIASl-------------------------TDPDSldmhktswlsmENSLI--------YEPLLTRDa-tGKLQPR 84  Brevibacillus b...
ZP_01724303   42 KNTLVISSv-------------------------REPDTidvhk-ttwvdNSTANi-------YDTLLKRDl-eGNIIPG 87  Bacillus sp. B1...
ZP_02142796   11 SGTAILAAsffanaamaqdii-iafsadelgatsYNPVT-----------SSNLNsat--sliYDRLVEQDa-dQSYHPH 75  Roseobacter lit...
ZP_03696036   21 GGVLALAGcadqadgdgn-------deifvdaldSDPGTldl------heTNRVPesmcltpvHERLFTIDp-dLEPQPW 86  Natrialba magad...
NP_618776     21 GAMIITAGclgqsaqtedn----vqedniqtlivAGPADfds------riEMKMNv-------YDVFLDINa-nGKTIPG 82  Methanosarcina ...
YP_710626     95 -LATSWEVASDlkTYTFKLREGVTFTDGTPFDAAAVKANFDRIVDkktksqyaatllgpytgTDVVD---AHTVKVNfs- 169 Frankia alni AC...
NP_125835     97 -LAESWEISEDgkVITFHLRKGIRDALGNPITAEDVKFVFDRLMNpetrspmaplvlgplkeVKVID---DYTVQLIyke 172 Pyrococcus abys...
YP_001433900 114 -LAREWSRSDDatTWTFKLVSGVKWHDGTPFTAQSVADYFDYIRDnpvgsgpg-slkavigsAKAVD---ETTVELTlt- 187 Roseiflexus cas...
ZP_02189938   68 -LAKSWTVSDDgkLYTFKLRDDVTFCSGKKFTAKDVKASIDRWLDpatkgvvk-nragdvkeIRAVD---DYTVEYElt- 141 alpha proteobac...
YP_002772101  97 -LASEFKISEDgkTYTFTIRSDVTFHDGTPLTAKSFKDTFERIKNpktkaklagivmmpvksVSAPD---DKTLILElh- 171 Brevibacillus b...
YP_002773614  85 -LAEKYEISQDgkVWTFILRKDVRYHSGDPMTAASVKDSFDRLLTispvkgl----agpiekVEATD---EHTLKVHfs- 155 Brevibacillus b...
ZP_01724303   88 -LAEKYDISDDgkIWTFYLDENVTFHSGEPLTAEAVKKSFERFLEysavkf-----lagpvdKMEVD---GQKLMIYft- 157 Bacillus sp. B1...
ZP_02142796   76 -LATSWEEAADglSWTFQLKDGVTFHDGTAFNAQSVADWIPDFADtenayl-----vgavasVEVID---ELTVKFVms- 145 Roseobacter lit...
ZP_03696036   87 -LATEYETNDDetEYVIQLEEGVEFHDGTEFNADVAKWNLERAEEnspda-------wqfgtLEEIDatgDYELTFHfe- 157 Natrialba magad...
NP_618776     83 hLVSSWNESDDglTYTFQLNKGIEFHDGTQWNASSAAWFLEWCSQgprkndi---afskisdVSEVD---EHTIQVTlk- 155 Methanosarcina ...
YP_710626    170 --kPFAPFLQGast-pnLGFYSTrslshgpdalcaggsaIVGTGPFVFTSYTKgQSVVLTKNPKYNWapqq---aahtGA 243 Frankia alni AC...
NP_125835    173 pygPALPFLATmp---pLGIFSKefyekvg--pvqfgqtPAGTGPYYVVKWVRgAYIEYKRNPYWKReyrpdpalknpGP 247 Pyrococcus abys...
YP_001433900 188 --aPRPDLLIElad-pgMGIGNAaylkrvg---adagfnPVGTGPFKFKEWVRgSQIVLERNPEWTWgspl---fkmsGP 258 Roseiflexus cas...
ZP_02189938  142 --qPYSELLFQmtq-hfHTIINAdevaalg--edfgvkgFDGTGPYCFVSWEPrNELILKKHEAYKWgpaf---yankGP 213 alpha proteobac...
YP_002772101 172 --ePNVSILEDl----gIGVTQPlsmkaiekygeeygrnPVGMGPWKFESWKAgEGVTLVRNEAFKWampl---denqGP 242 Brevibacillus b...
YP_002773614 156 --qPFAPFVNVi----vGGLVSPldakkakelgdgfadnPSATGPIIFDKRERgASLTYKKNPDYNWgpey---aankGP 226 Brevibacillus b...
ZP_01724303  158 --ePFAPFASGl----tTAYLAPmdpkalddygedfgknPSASGIFKFEERVRgSSITYMKNEDYNWgppf---vdnkGA 228 Bacillus sp. B1...
ZP_02142796  146 --rPEPNFLFNlss-sfMGIPGQvafdelg--ddfgvtgAVGTGPFRMESFTIgLQTVLTRNDDYAWasnl---senqGP 217 Roseobacter lit...
ZP_03696036  158 --ePHPLFPQYlan-vqMGFASReaveaag--ddygqeeVVGTGPLVFEEWVRdDEIVYSRNEDYDRgpdf---lsndGP 229 Natrialba magad...
NP_618776    156 --ePYGAFIKSlssesnSHVIAPtsvepaws-ndgeivsFIGTGKFEVENYVKaQSAEFVRHDPASG-----------EG 221 Methanosarcina ...
YP_710626    244 AYLDKVTFRFLtedtVRVGAVTSGQVDVATsippsdtr------tveadkglQIRk--VEDAGg-AYNVYLNtahgPLDD 314 Frankia alni AC...
NP_125835    248 PYIETIRFRIIkepfTLVSEFKAGNIHVLLdvppefy--------kdlandpNVEm--IPALEyvLHYIGFNcqkyPFND 317 Pyrococcus abys...
YP_001433900 259 PLIEEVVFRFSseaqTRLAALEAGEVDFVDllpfqdvv------rvrtdprfTVTg--VLLPGm-PQMNYLNtslaPTDD 329 Roseiflexus cas...
ZP_02189938  214 AKVDKLIWKIIpednNRVAGIQANQGDATQyipywav--------dqleanpQISvtkAPSYFw-TYFVGFKitreIADN 284 alpha proteobac...
YP_002772101 243 PRPDKLVIKTIpdksVMLAALENGTIDVAFdvpvkdikk-----yrnnpkyqVLE---LFRAGi-PLSLYMNltkpEFQD 313 Brevibacillus b...
YP_002773614 227 LQFDSMMFRFMkdddTRLMEFKKGTVHVLYdappnsva------eletlpgvKIEk--VMDIG--NKYIALNnkhpLFSD 296 Brevibacillus b...
ZP_01724303  229 PGFDKYEFRFItdddTRVLEFKKGTTQIMTnvppnyik------dlettegvKIDr--MFEQG--ITYLGFNnkkpMFQD 298 Bacillus sp. B1...
ZP_02142796  218 AHIAQITFREVpdqsTAFLELKTGGIDLLLgvptdfl--------qileveaNIAv--IQMPGtgINYMPINvtapPFDD 287 Roseobacter lit...
ZP_03696036  230 INFEEYHVRIVpeptTLLNEVTVGNVDGSMmiaasdae------dveahdntQLE---RVDDAh-PTFLSINveaePTDE 299 Natrialba magad...
NP_618776    222 TLIDRISYRVIpdsyASVSALRAGDVDIIGvadhhstvpyeqipqmmndpdiIVE---KQSYGr-YQVVELNckegALSD 297 Methanosarcina ...
YP_710626    315 VRVRRAIQLGANVDQAVKTVYf-GQYARawspltpatps---ydktltnaiaFDPTAAGKLLDEAGWtg-rDGQGYRTKD 389 Frankia alni AC...
NP_125835    318 TRVRQAINMAINREEIIKYALegLAVPVhgplvpsmngysekmeeyakqkypYDPEKAKQLLAEAGWvdrdGDGILEDKN 397 Pyrococcus abys...
YP_001433900 330 INVRKAIIYATDKQGIIESVYfnMVEPAygplsrvfpe----yepaleqmyeYNPEKAAQLLEEAGWl--pGPDGVRVKD 403 Roseiflexus cas...
ZP_02189938  285 IEVRKALNLAVDQKAIAEGPFfgKAEPAyayihpdvldy--dkkdintslfgYDPEKAKAILEAAGWk--mGDDGFRHKD 360 alpha proteobac...
YP_002772101 314 IQVRKAFHMLVNKQAMVQAVLm-GEGEVaqsflspstlg--ydkslekygypYNVEEAKKLLDAAGWk--vNGEGLREKD 388 Brevibacillus b...
YP_002773614 297 VRLRKAVALSVDRDPLVQVALngFGKPVygplaptiygyseaieskakqlytRDLGKAKQLLAEAGWtd-sNGDGIVDKD 375 Brevibacillus b...
ZP_01724303  299 KRVRQAIALGINRDPLVEFALegYAKPLfgplpqsipgysekvegeaaqkytQNVEKAKSLLEEAGWkd-tNGDGIVEKD 377 Bacillus sp. B1...
ZP_02142796  288 ILVRQATGLAINQEAIVASIYngVGAPAhnflisslpe----aqvdpalnvsYDPDRAMALLDEAGWi--mDDGGVRMKD 361 Roseobacter lit...
ZP_03696036  300 VEVRQAMAYAVDQEAIVNAAFhgEGYPIyslcppmavggl-deataretgyeQDLDTARELLDDAGWen-dEEGEVRTRN 377 Natrialba magad...
NP_618776    298 IRLREAINLGLDRDKMVKELLasAAEPAysvvspaypw----asnlagteytYDPEKAKNLLDQAGWvv-aGADEIREKD 372 Methanosarcina ...
YP_710626    390 GKRLTVNWPWNpphtreqrEVVAQAIQADLKKIGVEVTRPaldIGAYVSLALNgn------yDLYDFSWtr---fEPDIL 460 Frankia alni AC...
NP_125835    398 GNKFIVEMWIStge--leaPKVAQIIQAQLAKIGIKVKIRtveESSFTDLVSKgl------hQMYLFRYgl---qDAQIL 466 Pyrococcus abys...
YP_001433900 404 GRRLEVTIVENkg-----wNDWVYVLQANLQAIGFDAKVLttqGPSNTEAIASgkyhvpamgDVFASASq----mTRDWH 474 Roseiflexus cas...
ZP_02189938  361 GKKLKLVAYSFtn----iwQQIMEAMQGDMRKVGADLEIQvfdATVIWGKLKTqd------fDLFTMSYpy--vsAGDAM 428 alpha proteobac...
YP_002772101 389 GKVFTLSFLSSar-----fELQAQLLQAMLGEVGIKATIQnleESAFSDGQMKgn------fDVTMVTYsy---dDPDAL 454 Brevibacillus b...
YP_002773614 376 GKPLSVEMLVSqep---afQRAVQILQSQLKEAGIDMKISvqeMTTIKERISKks------yDMALMYYgw---fDADIL 443 Brevibacillus b...
ZP_01724303  378 GKPFSFEIWLSdep---vmQRIVQILQGQLKEIGIVVNISvqePASISANTPKgl------hDAILNTYgw---sDPDIL 445 Bacillus sp. B1...
ZP_02142796  362 GEPLSVKLFTQngt---efTALTQVVQAQLAEIGMEAVITvfdSSTIRDEYKEnr------hQLAVRGYdw---nNSDIL 429 Roseobacter lit...
ZP_03696036  378 GDDLSVSFFAFeme---pySSIGEVTQDMLSQVGFEANLEileSGTLYDRVEGge------hNLVTMALsgg-yiANNTL 447 Natrialba magad...
NP_618776    373 GQKLTLTYIVPqge--ansDSIAVYIQSELKKIGVEVDILvleSGAAGEERQKgn------yDMYLHHSwgvpglPEGPL 444 Methanosarcina ...
YP_710626    461 r---gFFNSASlpatggqnaanlkDPQVDTWTDAGaatlDRAKRDDLYGKVQHRVVVdDAVVLPIYIPtkLVAIAT---D 534 Frankia alni AC...
NP_125835    467 l---yMFHSKKgvkr-----mffyRKDLDEALDKMgttvDPEERQKYIEEAEKILID-GAPMVPLYARkvFLAYRKd--V 535 Pyrococcus abys...
YP_001433900 475 segygTFPSGHflk-------gedGARLDRMLKEAeteiDPEKRIEKYREIQKFIME-QALMVPIFELyfYVAHAN---N 543 Roseiflexus cas...
ZP_02189938  429 n---lYFPSENrptpn---rvnwaDDNTDKWLSEGraalTPEARYEAYAKVQKQVHD-AVVWIPLVHEpmFVAAGP---R 498 alpha proteobac...
YP_002772101 455 y---qSFHSSQigagfn--isglkDGKLDALLTKGrattETEARKQVYVDAQKHLLE-QAYVVPIYYDklFVVVSS---R 525 Brevibacillus b...
YP_002773614 444 y---lIFEKSNstsr-----thynNPELDVLLNKGrlemNEQARLKIYEDAQEILVN-DMPWVPLWVSe-TVIATR---G 510 Brevibacillus b...
ZP_01724303  446 y---mLFGKGSslrm------hyePEELHNLLTKArqtmDMEERMKIYEEAQQFLVE-ESPWVPLFVRe-NVTAYR---D 511 Bacillus sp. B1...
ZP_02142796  430 d---wFFSGERlgypnvsmwsdveGQRLNDVAMKEs--lNSDQRIANFTAYHEYVLS-QHLFVPIYQPtqNIAYNSdrvN 503 Roseobacter lit...
ZP_03696036  448 a---sTLHSQNyapdggsnyslyqSDEYDEIIDQAevepDDAEREALLHEAQEHILE-EVPVVPLVGFvkFYAAKNe-iS 522 Natrialba magad...
NP_618776    445 t---gKYHSTWgswp-----vsyhDAELDQLIETA----IATGADEDYSAAYLYIQE-KYACMPLYDIe-KIAAYRk--A 508 Methanosarcina ...
YP_710626    535 VSGL 538 Frankia alni ACN14a
NP_125835    536 VEGI 539 Pyrococcus abyssi GE5
YP_001433900 544 LKGF 547 Roseiflexus castenholzii DSM 13941
ZP_02189938  499 LKPI 502 alpha proteobacterium BAL199
YP_002772101 526 VKGV 529 Brevibacillus brevis NBRC 100599
YP_002773614 511 VKGF 514 Brevibacillus brevis NBRC 100599
ZP_01724303  512 INGF 515 Bacillus sp. B14905
ZP_02142796  504 VPDP 507 Roseobacter litoralis Och 149
ZP_03696036  523 VDAW 526 Natrialba magadii ATCC 43099
NP_618776    509 VKGF 512 Methanosarcina acetivorans C2A
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