1JET,1OLA,1B3L,2Z23


Conserved Protein Domain Family
PBP2_OppA

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cd08504: PBP2_OppA 
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The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold.
This family represents the periplasmic substrate-binding component of an ATP-binding cassette (ABC)-type oligopeptide transport system comprised of 5 subunits. The transport system OppABCDEF contains two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. 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: 173869
View PSSM: cd08504
Aligned: 316 rows
Threshold Bit Score: 274.817
Threshold Setting Gi: 160945308
Created: 27-May-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
peptide binding
Conserved site includes 11 residues -Click on image for an interactive view with Cn3D
Feature 1:peptide binding site [polypeptide binding site]
Evidence:
  • Structure:1JET_A; Oligopeptide binding protein from Salmonella typhimurium binds a tripeptide (Lys-Ala-Lys), contacts at 4 A.
    View structure with Cn3D
  • Structure:1B3L_A; Oligopeptide binding proten from Salmonella typhimurium binds a tripeptide (Lys-Gly-Lys), contacts at 4 A.
    View structure with Cn3D
  • Structure:1OLA_A; Oligopeptide binding proten from Salmonella typhimurium binds a tetrapeptide (Val-Lys-Pro-Gly), contacts at 4 A.
    View structure with Cn3D
  • Structure:2Z23_A; Oligopeptide binding protein from Yersinia pestis binds a tripeptide (tri-Lys), contacts at 4 A.
    View structure with Cn3D
  • Citation:PMID 8747465

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                  #                                                     
1JET_A        13 QTLVRNNGse--vqSLDPHKiegvPESNVSRDLFEGLLISDv-eGHPSPGVAEKWENkd-fkVWTFHLREnAKWSDGTPV 88  Salmonella typh...
AAC34992      35 EKLAFKVYiggapsSLDPHLvdetIGARILEQIFSGLLTLNtktGKLKPGLAKNWEAskdkkTYQFYLRDnLFWSDGVEI 114 Borrelia burgdo...
NP_212462     31 EKIVFRVSnlsepsSLDPQLstdlYGSNIITNLFLGLAVKDsqtGKYKPGLAKSWNIsedgiIYTFNLREdIVWSDGVAI 110 Borrelia burgdo...
AAC46281      27 DDIVFGVGigneptSLDPQFcsdrLGNLIINELFVGLLRGDpktGGYRPGLAKNWDIsydntCYTFHLRDdIYWSDGIKI 106 Lyme disease sp...
AAC46283      28 VSFKISLGae--psSLDPQLaednVASKMIDTMFRGIVTGDpntGGNKPGLAKGWDIssdgtVYTFNLREkITWSDGVAI 105 Lyme disease sp...
NP_219023     41 KEFVVSFSpy--rpVLHPHVasrvDEAQLLTALYEGLVTYDpydLHPIPALAQHWSVstdglTWTFYLRDqIFFQNGDPI 118 Treponema palli...
YP_001396830  40 NSLVYNLGel--pdDLIMLDsdnvRQKDILANAFEGLVSSDa-nGKIIPSLAESWSVsdegtSYTFKIRKnAKWSNGTDI 116 Clostridium klu...
YP_878899     36 DYLVYSVNsm--pqDLLLLDdnsiRKKDLQIALFDGLVSMDe-kGKIVPSLASSWSVskdklSYTFKIREdARWSNGEKI 112 Clostridium nov...
NP_972651     25 KELNISITsg--ipMLHPHTafdaGEAQILTALCEGLFVYDpytLQPVPALAEKYSVsg-grTWRFTIRKdAKFENGKPI 101 Treponema denti...
ZP_02613752   34 DYLIYNIEtm--pkDLIMLEdgsqREEDLLLSLFDGLVGLDr-sNNIVPELAEKWEVskdgiDYKFYIKDnLFWSNGKEI 110 Clostridium bot...
Feature 1                                                                                        
1JET_A        89 TAHDFVYSWQRLADPntaspyasylqyghianIDDIIAgkkp---atdLGVKALDDHTFEVTLSEPvPYFYKLLVHPSVS 165 Salmonella typh...
AAC34992     115 TAEGIRKSFLRILNKetgstnvd-mlksiiknGQEYFDgkvs---dseLGIKAIDSKTLEITLTAPkPYFLELLLHYAFM 190 Borrelia burgdo...
NP_212462    111 TAEEIKKSYLRILNKktaamyan-likstiknAQEYFDetvp---eseLGIKAIDSKTLEITLTSPkPYFPDMLTHSAYI 186 Borrelia burgdo...
AAC46281     107 TASTIRDSYIMALENeldephin-lltskiknAQEFYEtkln---adeVGVKVINEQTLEITLSRPaRYFLDMLTHPIFI 182 Lyme disease sp...
AAC46283     106 TAEGIRKSYLRILNKetgskyve-mvksviknGQKYFDgqvt---dseLGIRAIDEKTLEITLESPkPYFIDMLVHQSFI 181 Lyme disease sp...
NP_219023    119 TAETFQQSWLNLLNPewnvpyas--fldavegARAYRSgttadshtvgILVEGSDKKTLVVKLAYPaGHFIQMLCHHAFA 196 Treponema palli...
YP_001396830 117 TSYNFVDFFSHILSVnvkniyga--qldcifgAEDYRKgkcd---fknVAVTAIDKDTLSIRLNYPcNYFLNILAQPIYS 191 Clostridium klu...
YP_878899    113 APQDFVEFFSRILKEkdntyah---elqcifgVKEYLEgeks---fqqVAINPGKDNTLEIRLNYPcDDFIKILSKPVFT 186 Clostridium nov...
NP_972651    102 TAQTFVDSWLNLLNPagnhpyas--lldcidgAADYRNgklk--nknqVGIKAESEQVLLVTTNTEiEHLPNILCHHAFS 177 Treponema denti...
ZP_02613752  111 AARDFEKFFKDILIYckennirf-nelnsvygVKDYLAngn----ldnIAIKAKEDNILEIRLNNKdPYFLSTLSKPKYK 185 Clostridium bot...
Feature 1                                                                                        
1JET_A       166 Pvpksavek--------fgdkwtqPANIVTNGAYKLKNWVVnERIVLERNPQYWdnaKTVINQVTYLPissevtdvnRYR 237 Salmonella typh...
AAC34992     191 Pvpvhviek--------ykgnwtsPENMVTSGPFKLKKRLPnEKIIFEKNERYYnakEVELDELVYITsdndltvynMYK 262 Borrelia burgdo...
NP_212462    187 Pvpmhivek--------ygenwtnPENIVVSGAYKLKERSInDKIVIEKNEKYYnakNVEIDEVIFYPtegs-vaynMYI 257 Borrelia burgdo...
AAC46281     183 Pipthivkk--------fgnkwtsSENMVTSGPFKLKRRILnEEISLEKNEKFYdakNVAINELIFVTindtrriysMYE 254 Lyme disease sp...
AAC46283     182 Pvpvhvtek--------ygqnwtsPENMVTSGPFKLKERIPnEKYVFEKNNKYYdsnEVELEEITFYTtndsstaykMYE 253 Lyme disease sp...
NP_219023    197 AvhptqlasvgtlhartasasahkPFHPIASGPFELQQMQA-DRVVLRVNTRYWdrdALALHAIVALIaqdpaardaGFN 275 Treponema palli...
YP_001396830 192 Lriidyki----------inwkkyYNSILYSGSFTISNVSDeQEITLKKNSKYWnasKVKSNTIVVTSlktsesalaGFD 261 Clostridium klu...
YP_878899    187 Lkrnfynl----------knwrseYKNIDYSGAFFIENIYDdGEISLKKNNMYWdekNVVSNRIHIKEskvmastlaQYK 256 Clostridium nov...
NP_972651    178 AveasqleaalkfsnierieklrdSFKPISSGAYKIKKFSE-KELILVKNENYWdkdNVQIPQINLFLdlskedaieKFN 256 Treponema denti...
ZP_02613752  186 Lrkidkkn----------knykktFNEIPYTGAFCINKIEK-DQITINKNNRYWdkeNIKINRIVLKSiqnseealaHLK 254 Clostridium bot...
Feature 1               #                       #                                                
1JET_A       238 SGeiDMTYnnmpielfqklkkeipnEVRVDPYl--cTYYYEINnqka-pfnDVRVRTALKLALDRDIIVNKVKn------ 308 Salmonella typh...
AAC34992     263 NNeiDAIFnsippdiv--neiklqkDYYQHKSn--aIYLYSFNtkik-pldDARVREALTLAIDRETLTYKVLn------ 331 Borrelia burgdo...
NP_212462    258 NGelDFLQgaeknnl---eeikirdDYYSGLKn--gMAYIAFNttik-pldNLKVRQAISLAIDRETLTKVVLk------ 325 Borrelia burgdo...
AAC46281     255 HNeiDAIFnniplsli--nelilreDFYSADIn--qIGFFSLNtnvk-plnNVKVREALALAVDRETLTYRVLd------ 323 Lyme disease sp...
AAC46283     254 NEelDAIFgsippdli--knlklrsDYYSSAVn--aIYFYAFNthik-pldNVKIRKALTLAIDRETLTYKVLd------ 322 Lyme disease sp...
NP_219023    276 DGsiHWISgalehs-----slqdaaTLQIVPLl--aTEYLCFKtahe-ptcNATLRKALLLATPVEELTARYLf------ 341 Treponema palli...
YP_001396830 262 NYriNIFTdpplgei----eniekkDKYITDTel-kGTGIVFNlkgkgivsNVNFRKAVSLSIDRNNIVKNILkdtvtla 336 Clostridium klu...
YP_878899    257 SNrvDVFCdynvlq-----ngdiedEKKYTKQligdGISLNFNlnkdnfvkDIKFRKAIKCAVDKEEIKKELGevf-ket 330 Clostridium nov...
NP_972651    257 IGkiHWLSrsdvis-----kigdqrCVNIDPLf--aTDYFFFKtssp-nikDAEFRKALLLAVPYEELRNGYPi------ 322 Treponema denti...
ZP_02613752  255 TSklDLFMnppiae-----innlnkEGLISKKlsleTGNIIFNkkd---yiDLNLRRAIDSCISREDMCSKLLygksvpa 326 Clostridium bot...
Feature 1                                                                                        
1JET_A       309 QGDLPaysytppytdgaklvepewfkwsqqKRNEEAKKLLAEAGFtad-kplTFDLLYNts-dlHKKLAIAVASIWKKn- 385 Salmonella typh...
AAC34992     332 DGTVPtreitpdlen------ynygkklalFDPEKSKKLLADAGYpngkgfpMLTLKYNtn-etHKKIAAFIQNQWKKi- 403 Borrelia burgdo...
NP_212462    326 GSSDPtrnltpkfdd------ysygknlilFDPENAKKLLAEAGYpdgkgfpTLKYKISe---gRPTTAEFLQEQFKKi- 395 Borrelia burgdo...
AAC46281     324 NNFKAtrkispninn------ynygkklkpYNPRKAEKLLAEAGYpdgknfpTLTIKYNkn-dlEKEVASFIQSQWKKv- 395 Lyme disease sp...
AAC46283     323 NGTTPtrratpnfss------ysyakslelFNPEIAKALLAEAGYpngngfpILKLKYNtn-gaNKKICEFIQNQWKKn- 394 Lyme disease sp...
NP_219023    342 PARTLvtpftgyp----------vppvvheYNPARARALLAEAKIggktartPLKILVSdt-eaCRALALELQKAWTA-- 408 Treponema palli...
YP_001396830 337 NSYIPgcvdnglesn-----finksffsesANEEAALEVMKNLDYnde--kkSLKLIYVns-veNKKVCDEIAKNLKKy- 407 Clostridium klu...
YP_878899    331 YGYLPnssln---------------stnrsYNIKSAEELLKDSKYng----eVVKIVYAnnednNKKVINSIEKNLKK-- 389 Clostridium nov...
NP_972651    323 KAETLifplagyp----------kiqgvneYNLQKAQEIINKLNLneeqkkvVIKIPENt---yYQELAEILSAAWAK-- 387 Treponema denti...
ZP_02613752  327 IAYVPnniaenddis------ygknyfslnKNLQRAKEFLDKSEYkke--kkDLKIISIed-piSNKIANSIIGELKEsl 397 Clostridium bot...
Feature 1                   #               # #####                                              
1JET_A       386 LGVNVNLEnqeWKTFLDTRHQgtFDVARAGWCADynePTSFLNTMlsdss--nntahYKSPAFDKLIADTlkvaDDTQRS 463 Salmonella typh...
AAC34992     404 LNINLMLTnenWPVLTNSRNTgnFEIIRVGRIGEyldPHTYFTIFtrensq-lasygYSNLEFDKLIRESdlekDPIKRK 482 Borrelia burgdo...
NP_212462    396 LNINLEIEneeWTTFLGSRRTgnYQMSSVGWIGDyfdPLTFLDSLfttenhflgaykYSNKEYDALIKKSnfelDPIKRQ 475 Borrelia burgdo...
AAC46281     396 LNIDVEIEpetWVNHISNILKgqYEISVRSWQGDyldPMAFFNIFetknsh-fasygYSNPELDELIIKSdleeDEKLRL 474 Lyme disease sp...
AAC46283     395 LNIDVELEneeWTTYLNTKANgnYEIARAGWIGDyadPLTFLSIFtqgytq-fsshnYSNPEYNELIKKSdlelDPIKRQ 473 Lyme disease sp...
NP_219023    409 LALAVEIWavrPETYREYVQDekYHVRIVSWVADfadPMAFLELFrkgsk--thstgWTHEEFEALLTRAgaepHVLRRW 486 Treponema palli...
YP_001396830 408 IKINVKCVgydLNSFNNEIKNgnYDMAEIYYEGYynyPLPFFQIWqssst--ynlygYSNIEFDNKFTGTvfekDVNKKV 485 Clostridium klu...
YP_878899    390 AKVNVDIQgysKQELKNIIDKgnYDIALLNYSGDstmPLTYLEKWisnsk--qnlfgYKNINFDNCILKAkvseNKLESQ 467 Clostridium nov...
NP_972651    388 IGVKTEVKlisLNAYYNSLKTndYDLGTITWIGDfadPLAFLEMFrpnsn--lndsdWKNQEFERIILKShaekDFKKRY 465 Treponema denti...
ZP_02613752  398 DINLNLVNckdENELEQKIKNgdYDLAFVRNKAKnndPLFFLLNFt-----------SDSLQYQDFLNKIkledNMWKKR 466 Clostridium bot...
Feature 1                              #                              
1JET_A       464 ELYAKAEQQLDKd-SAIVPVYYYvnARLVKP--WVGGYTGKd-----pLDNIY 508 Salmonella typhimurium
AAC34992     483 QLLRKAESIIIEkdFPAAPIYIYsgHYLFRNd-KWTGWNPNv-----sEVYYL 529 Borrelia burgdorferi N40
NP_212462    476 DILRQAEEIIAEkdFPMAPLYIPksHYLFRNd-KWTGWVPNi------AESYL 521 Borrelia burgdorferi B31
AAC46281     475 EILKKIEEIIIEndYPIIPIYSVagNYLFKNd-KWLGWNTNn------SERFA 520 Lyme disease spirochete
AAC46283     474 DILRQAEEIIIEkdFPIAPIYIYgnSYLFRNd-KWTGWNTNile--rfDLSQL 523 Lyme disease spirochete
NP_219023    487 ELLAQAERILLQe-AVVLPLSRLhaLHAVQRr-TVRGWYANvld--vhPFKFI 535 Treponema pallidum subsp. pallidum str. Ni...
YP_001396830 486 EMFKDMENLLLEd-MPIVPIYFNk-TVIVTRn-YVKDVYTNkmgniklDKAYL 535 Clostridium kluyveri DSM 555
YP_878899    468 KKFNEGEKVILEd-IATIPIGVY--KFIVCRkeYVEGLEVNsrgnvilKKAYI 517 Clostridium novyi NT
NP_972651    466 EMLSKAEELLLGe-SVIIPISYRlsVNIIDIy-SIGGWYSNaid--ihPFKFI 514 Treponema denticola ATCC 35405
ZP_02613752  467 EYINKAQDVLAEd-LYTIPVCFFy-DMLCKRs-RVQGQYITidgnviiKKITL 516 Clostridium botulinum NCTC 2916

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