3DRF,3FTO


Conserved Protein Domain Family
PBP2_Lactococcal_OppA_like

?
cd08510: PBP2_Lactococcal_OppA_like 
Click on image for an interactive view with Cn3D
The substrate binding component of an ABC-type lactococcal OppA-like transport system contains
This family represents the substrate binding domain of an ATP-binding cassette (ABC)-type oligopeptide import system from Lactococcus lactis and other gram-positive bacteria, as well as its closet homologs from gram-negative bacteria. Oligopeptide-binding protein (OppA) from Lactococcus lactis can bind peptides of length from 4 to at least 35 residues without sequence preference. The oligopeptide import system OppABCDEF is consisting of five subunits: 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 also is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 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
?
PSSM-Id: 173875
View PSSM: cd08510
Aligned: 25 rows
Threshold Bit Score: 625.833
Threshold Setting Gi: 21282602
Created: 27-May-2009
Updated: 2-Oct-2020
Structure
?
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:3DRF_A; Oligopeptide binding protein (OppA) from Lactococcus lactis subsp. cremoris MG1363 binds an endogenous peptide, contacts at 4 A.
    View structure with Cn3D

Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                        
3DRF_A        32 GGNLKVAYqsdspMKAQWLSGLsndatFATMSgpgggQDGLFFTDs--gFKFIKG---GAADVALDkesKTATITLRKdL 106 Lactococcus lac...
ZP_03625644   39 DAQLKYAWvspttSSGLLIDELtenttDSTFGgf--vDISMFGYDg--eRKLDDSg-lAKAEFDVKgkkITISLTGKD-Y 112 Streptococcus s...
ZP_02093737   77 NGTLKIGIigespFKGVFHEAFaqdnfDMTIMnw-vgMGGFFDSDp--dYKNGNT---GQGKIEFKpkeKKAIITIHEkA 150 Parvimonas micr...
EEO37084      51 VDTLKVAVvssspYKGIFNGFLyssgiDNEFMqy--tMNGAFPTNp--dFTLVLDsdeTPIKVTVNpeeKTVTYKINPkF 126 Fusobacterium s...
NP_645690     44 GGTLNVALta--pPSGVYSSLLnsthaDAVVEgy--fNENLLTIDk--kIRPKSY---IASWKDIEp-aKKIEFKIKKgI 113 Staphylococcus ...
ZP_04448880   46 GGTLKIAAvagepFSGAFSSLVadqstDLSVVeg-yiNTGLFEYDe--nLQIKDT---GLASAKLDpenKKVTITIRKdQ 119 Catonella morbi...
ZP_02093738   66 NATLKVAYindspFTGIFHQAFasgnpDMEILay--sTNGTFKIDe--nYRLVNG---GGADIEFKpeeKKAIITIHEkY 138 Parvimonas micr...
ZP_04448881   48 GGVFKYALvg-dpFSGALSSLYaeksnDMTITgf--iNPGLYGSDg--dYKIDDS---GLAKLTFDqanKKVTIKIPEgV 119 Catonella morbi...
YP_001691583  75 GGTFRVGIptdspFKGIFNNTLyddnyDWNIIgp--tMYTAANAGe--sLELRDS---GAEKFEWDekaKTATIKLSDsF 147 Finegoldia magn...
ZP_02172067   65 GGTVTYGYts--pFAGLLDWAWyegqdDSLALsl-fnGEALYQVRseneFELEPS---LAREWEWSddnTTVTFHLEEgV 138 Bacillus seleni...
Feature 1                                                                                        
3DRF_A       107 KWSDGSEVTAKDYEFTYETIANp----aYGSDRWtdslaNIVGLSDYHTGKAKtISGITFPDgenGKVIKVQFKEmkPGM 182 Lactococcus lac...
ZP_03625644  113 KWSDGEPFTINDYIFTIKSMASk----dYTGIRFddkflNIEGMQEFVDGKASdISGIKKVD---DYTVELTVKEmsPSM 185 Streptococcus s...
ZP_02093737  151 TWSDGVPVTAKDFLRYYLIIGHk----dYEGVRFgtdylNVVGMKEYHDGKAKdVSGVKIID---DKHLEITFKEfdHSI 223 Parvimonas micr...
EEO37084     127 KWSNGEPVTTKDIVKTYEIVANqkyiesSSSSRFnknrkKIVGIQEYNEGKADkISGLEVID---DSTMKIHLTEvtPSV 203 Fusobacterium s...
NP_645690    114 KWHDGNELKIDDWIYSIEVLANk----dYEGAYYps-veNIQGAKDYHEGKADhISGLKKID---DYTMQVTFDKkqENY 185 Staphylococcus ...
ZP_04448880  120 KWSDGQPLTIDDVIAPYYIIANk----dYTGIRYgddfkNVVGIEDYHDGKSDtISGLKKID---DYTLEISYKTfsASM 192 Catonella morbi...
ZP_02093738  139 TWNDGTPVTSADFLEYYKIVAHk----dYTGVRFdddmrNVVGIEEYNKGESKeISGFKTLS---DKKFEIHFKKfnPGI 211 Parvimonas micr...
ZP_04448881  120 TWTDGQPLTIEDVIYPYYVVGHk----dYTGIRYgsdfkNVVGMEDYHEGKSDtISGLKKVD---DYTLEISYKEfsASM 192 Catonella morbi...
YP_001691583 148 KWNDGKPVTAKDIIINYLIIGHk----dYPGVRYdddmiNIVGMEDYHAGKTKdISGVKEID---NKTVQIQFKEwvPSI 220 Finegoldia magn...
ZP_02172067  139 MWHDGVELTAEDFKFSYETIAHp----dGNTARQsn-vdRIVGYDEYRAGETDeLAGVEVID---DYTFSVEFKEvqANN 210 Bacillus seleni...
Feature 1          #                                                                             
3DRF_A       183 TQSgngyfletvaPYQYLKDVAPKDLaSSPKTTTKPLVTGPFKPENVVAGESIKYVPNPYYWg-eKPKLNSITYEVVsta 261 Lactococcus lac...
ZP_03625644  186 MYAggdvpayiqpEHIYKDIPVADWEkSEYSRTAKLVGMGPWKIKEIVNGESITYVPNEYFFkgtKPKTSSLKIDIVspd 265 Streptococcus s...
ZP_02093737  224 YWGkgip--ynpvPDHVYKDIPIKEQeSHEATRKHPLSCGSHVIKEIVPGQQVVAEANPYYAf-gKPKTPRMEIKIVpss 300 Parvimonas micr...
EEO37084     204 YWGgnfv--sefvNAKQFEGVPMDKIiESPALRKNPLSYGPYYIKDIVQGEKVIFEANPYYYr-gEPKIKTIEMEILpps 280 Fusobacterium s...
NP_645690    186 LTGfitg---pllSKKYLSDVPIKDLaKSDKIRKYPIGIGPYKVKKIVPGEAVQLVKFDDYWq-gKPALDKINLKVIdqa 261 Staphylococcus ...
ZP_04448880  193 KQVgggis-pyvePKHIYDKIAIKDIaDSDQVRVNPVGMGPFRVKSITPGEAIVLESNEYYFk-gKPKVDGAVIEVVnps 270 Catonella morbi...
ZP_02093738  212 LWGggip--fepvPSHKLKDIPVKEQeAHDITRKNPLSPGPYYIKEIVPGQQVVFEANPHYYk-gQPKVKKVVWKIVpss 288 Parvimonas micr...
ZP_04448881  193 LQAgggvs-syvePKHILEKTPIKDLeDSEQVRTNPIGFGPFKVKSITPGESVVFERNDNYYk-gKPKVAGLQVDVVnas 270 Catonella morbi...
YP_001691583 221 KWGagiw--aepnSYDQLKDIPVKDIiSSDPVRKNPKSAGPFYISNVVPGQSVEFSANEHFWg-gKPKIDKVVMERVpss 297 Finegoldia magn...
ZP_02172067  211 LANlws----ypmSVNHLGHLEVSEMeDADEIRRNPVGLGAFVVDNVVPGEMIEYSAFEDYWq-gAPNLDGVVYRIVdge 285 Bacillus seleni...
Feature 1                                                                                        
3DRF_A       262 ksvaALSSSkYDIINgmvssqy-kqvknlkGYKVLGQQAMyISLMYYNLGHYDaknsINVQDRKTPl-qDQNVRQAIGYA 339 Lactococcus lac...
ZP_03625644  266 tivsEMKAGnYDIAEmpvdqld--sykdvsNLNIVGQLESsYEYISFNLGKYDeaanKNVMDEKAKm-nDVKLRQAIAYA 342 Streptococcus s...
ZP_02093737  301 qvvaASKSGeYDIIDsfssdly-ekfaalkNGKIASNYYGgYNYLGFKLGKYDkdkgEVVTNPDAKm-aDKNLRKAMAMA 378 Parvimonas micr...
EEO37084     281 qqvaAIKSGkYDIVFspelnif-peienldNINILARKAMyFSYLGFHVGKWDaeknEVITDPNSKm-yDINLKRAMAYA 358 Fusobacterium s...
NP_645690    262 qiikAMEKGdIDVTNdatgamakdakssnaGLKVLSAPSLdYGLIGFVSHDYDkk-aNKTGKVRPKy-eDKELRKAMLYA 339 Staphylococcus ...
ZP_04448880  271 tavaEMKAGnYDLAElptdayd--tfkdasNFKTIGTVENtYSYIGFKFGSWNkdkeEVEMDPSKVi-qNKALRQAMAYA 347 Catonella morbi...
ZP_02093738  289 qivaALQAGeYDLTVglnsdly-skvkdlkNVKLGIQDELsYTYIGFKLGKWDntkkEVVTDPNAKm-aDVKLRQAMAYA 366 Parvimonas micr...
ZP_04448881  271 tavsEMKAGnYDYAAlpeetys--tykdasNFKTLGRLTNvYSYIGFHVGTWNke-kEQVQPDDSKpvsNKALRQAMAYA 347 Catonella morbi...
YP_001691583 298 qilaSLKAGkYDYIAggapsdtfkeiselkGYKVARFQDMaYTYLGFKLGKWDkakgEVVVDPNAKm-aDVNLRKAMGYA 376 Finegoldia magn...
ZP_02172067  286 lsgeLLAQGeVDVIEltggqal--plqdddRVYLEEIEALsYMYIGFKLGHWDdeegTAVMDNEKFq--SKELRHAFAHA 361 Bacillus seleni...
Feature 1                                                                                      # 
3DRF_A       340 RNVAEVDNKFSnGLSTPansLIPPIFk-qFTSSSVKGYekQDLDKANKLLDEDGWKLnks-tgYREKDGKELSLVYAARv 417 Lactococcus lac...
ZP_03625644  343 IDTKTAGKSLYnGLYHPaksLIISFFg-dIHDSELEGYs-YNPEKAKKLLDEAGYKDvdgdgiREGKDGKAFKITFAARk 420 Streptococcus s...
ZP_02093737  379 VDRDTINKKLQkGLSIPlyqIIPPMFs-tIYDKDYQGIk-YNLEEAKKLLDEAGYKDtngdgiREDKNGKPLKIKFAAMq 456 Parvimonas micr...
EEO37084     359 IDNDSIAKQFYhGLAMRapsPIAPVFt-kLRNPEVDGFk-IDLEKAKKLLDDAGYKDvdgdgiREGKDGKPFKINLAMMs 436 Fusobacterium s...
NP_645690    340 IDREKWIKAFFnGYASEinsFVPSMHwiaADPKELNDYk-YDPEKAKKILDKLGYKDrdgdgfREDPKGNKFEINFKHYs 418 Staphylococcus ...
ZP_04448880  348 FDADAVGQRFFsGLRFRantLIPSLFk-sVHASDLPGFt-YDPEKSKQILADAGFVDkdgdgfIEDPNGKPFTLKFLARs 425 Catonella morbi...
ZP_02093738  367 IDNNQVGEKFYqGLRRNatqLMIPAFk-eYYDESLKGYt-YDLEKAKKLLDEAGYKDtngdgiREDKNGKPFKIKFASMs 444 Parvimonas micr...
ZP_04448881  348 IDNDAIGKRFYeGLRVRansPIPSMFa-sYNDGSIEGYt-YQPEKAKQILADAGFVDkdgdgfVEDPNGKSFKLTFAAMs 425 Catonella morbi...
YP_001691583 377 VDNNAVGEKFYlGYRSQatsVIIPIFk-dYFNTDLKGYn-YDPEKAKKLLDEAGYKDvnndgfREDKNGKPLVIKFASMa 454 Finegoldia magn...
ZP_02172067  362 IDRQGIIDSFMeGYGTVinaPESVIRwsyPDESALNQYe-HDPDRARELLEEAGYEDvtgdgfVEDPNGDEFTVNFAAMn 440 Bacillus seleni...
Feature 1                                         #  ##                 ##         ##       # #  
3DRF_A       418 gd-anaETIAQNYIQQWKKIGVKVSLYngklmeFNSWVDHMTTPpganDWDITDGSWslaSEPSQQDLFsaa-apYNFGH 495 Lactococcus lac...
ZP_03625644  421 rt-eanEALVQQYIAWWKEVGLNVELYtgrtveGKSFYNSVQANd--pAIDMYAGGWstgYDPNPSGLWgsv-aaFNMSR 496 Streptococcus s...
ZP_02093737  457 gg-atqEPTVSFLIQQWKAIGLDVELTtgrlieFNSFYEKLGADd--pEIDVYMGGWstgSNPDPSGFYgkh-esFNFQR 532 Parvimonas micr...
EEO37084     437 gs-eiqEPLSQYYIQQWKLIGLNVELVdgrlldFNNFYDRLKADd--pAIDCFFAAFgygTDPQQMSLFgkn-sqFNKSR 512 Fusobacterium s...
NP_645690    419 gsnptfEPRTAAIKDFWEKVGLKTNVKlv---eFGKYNEDLANAs--kDMEVYFRSWaggTDPDPSDLYhtd-rpQNEMR 492 Staphylococcus ...
ZP_04448880  426 ss-diaEPLWSYFVDSWKQVGINVELLdgrlydFNSYADMLRSDd--qSFDVFEGAWgtgGDPNPTGFYskk-apFNYER 501 Catonella morbi...
ZP_02093738  445 gg-aiaEPIANYYIQQWKSIGLDVELTtgrlieFNSFYEKVQADd--pEIDIYQAAWgtgSNPNPTGLYgrk-aqFNFSR 520 Parvimonas micr...
ZP_04448881  426 gs-dvaEPITQYYLDAWKQIGVNIELYegrlleFNAFYDLLDSDa---DIDVFQAAMgvgGDPNPSSQFgrd-nqFNMMR 500 Catonella morbi...
YP_001691583 455 gg-diaEPLAKYYMQCWEQVGLKVELTggrlieFNAFYDKLKNDd--pEIDVFQGAWstgTNPDPSGLFskn-asFNYYR 530 Finegoldia magn...
ZP_02172067  441 apadiaEPRAQYIIQNLQDVGINAQLMdgqlldFNLFYDLVEEDd--sDIDIFMGAWglaTADPDLSGLwlstdfWNFTR 518 Bacillus seleni...
Feature 1                                                                       
3DRF_A       496 FnDSEITKDLNDIdsa--kseNPTYRKAAFVKYQEDMNK-KAYVIPTNFMlnYTPVNKRVVGM 555 Lactococcus lactis subsp. cremor...
ZP_03625644  497 FvSDENTKLLEAIssa--esfDDKKNVENYKAWQKYAHE-QAFAIPTFESesIVALNKRVKNY 556 Streptococcus suis 89/1591
ZP_02093737  533 FtSPELDKLLANIvsl--dntDPEVRKKHYAELSKYLINdEAIVVPVFSSttKAFVNNRVKKY 593 Parvimonas micra ATCC 33270
EEO37084     513 YtSETFEKALEAQisp--ealDEAKRIEIYHNYDKIFME-ELPVAPQLNKmeYIVVNKRVKEY 572 Fusobacterium sp. 2_1_31
NP_645690    493 TvLPKSDQYLDDAldfdkvgiDEKKRKDIYVKWQKYMND-ELPGLPMFQGksITIVNDKVRNL 554 Staphylococcus aureus subsp. aur...
ZP_04448880  502 WaDDKNEELLDALssd--kafDEAYRKEAFHAWQAYTNE-ELPAIPYLYRygIRSVNNRVKHY 561 Catonella morbi ATCC 51271
ZP_02093738  521 FsSEELDKIFDKInsv--eavDKDYRAKAYKEFANYMFE-NVPVVPTLFRkgIVAVNNRVKKW 580 Parvimonas micra ATCC 33270
ZP_04448881  501 WaTEENDKLLAAInsd--aafEDSARKKAYDDWQKYVID-EAPVIPTLYRhsLVSINNRVKNF 560 Catonella morbi ATCC 51271
YP_001691583 531 YtNPEMQKALDKIsdg---ktSDEDRAQAYKDFAKVMED-NVPLIPTLYReaLSPINKRVKKF 589 Finegoldia magna ATCC 29328
ZP_02172067  519 WvNEESDELIRAGvse--ealDFEYRQSVYQEWHQLFNE-ELPMIPISSPvnIYGIAADVGGI 578 Bacillus selenitireducens MLS10

| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap