1XOC


Conserved Protein Domain Family
PBP2_AppA_like

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cd08514: PBP2_AppA_like 
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The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus subtilis contains the type 2 periplasmic-binding fold.
This family represents the substrate-binding domain of the oligopeptide-binding protein, AppA, from Bacillus subtilis and its closest homologs from other bacteria and archaea. Bacillus subtilis has three ABC-type peptide transport systems, a dipeptide-binding protein (DppA) and two oligopeptide-binding proteins (OppA and AppA) with overlapping specificity. 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 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: 173879
View PSSM: cd08514
Aligned: 36 rows
Threshold Bit Score: 477.882
Threshold Setting Gi: 229539960
Created: 29-May-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
peptide binding
Conserved site includes 15 residues -Click on image for an interactive view with Cn3D
Feature 1:peptide binding site [polypeptide binding site]
Evidence:
  • Structure:1XOC_A; Oligopeptide binding protein AppA from Bacillus subtilis binds nonapeptide (VDSKNTSSW), contacts at 4 A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                #                                                       
1XOC_A        23 DLVVGSige-ptlFNSLYstDDASTDIEnm---lYSFLTKTDe-------kLNVKLS------------------LAESI 73  Bacillus subtilis
YP_845537     53 DWVIGNlgsepptLNPITstDLSASTIQey---iYETLIRRNpe------tMKLEPL------------------LAESW 105 Syntrophobacter...
NP_662515      1 MLGDADy------LNPVIgaSLTSSEITgl---iYPALLQGEfdtk--tglLNYLALekrlrsstgpdekspkgaLAKTW 69  Chlorobium tepi...
YP_344747     99 WFVQAFgag-lttLTPLVstDAYAAEVQgy---iLESLLTRHpe------tLDWQGL------------------LARDW 150 Nitrosococcus o...
YP_001997613  35 TLGVAAdf---dyLNPLLiqLSLSREVCth---iFPTLVRPQfdek--ngaVSFAPS------------------LAKSW 88  Chloroherpeton ...
NP_662306     46 TIVVAVsad-fdhLNPLLiqMSLAREVCtm---iYPQLVKPSfdek--sgaISYQPN------------------AAERW 101 Chlorobium tepi...
ZP_01857897  123 TINRHVgad-lksTNPIMgsSAVEFEVSsl---tGFGLFSFD---------WNFKPFav--------------sdTVVSW 175 Planctomyces ma...
ZP_01091691   99 TIVRHVggd-aksTNPLM--ISSVTEFD------VVGLMGIEiyg----fdWNMDPLan--------------sdYVVSW 151 Blastopirellula...
ZP_04429096  297 NWSNEQgelvisgIIPGKyrVLTGSEIYgkvkplADGAIEVTplseenplkQALPPGqts------------lvlKADEY 364 Planctomyces li...
YP_007102    124 VRKEATfrk-pdhLHPFSp-WLEVSSWNdl---cSISLASQEvg-----kyETMAPE------------------MAERI 175 Candidatus Prot...
Feature 1                                                                                        
1XOC_A        74 KEldg---glAYDVKIKKgVKFHD------GKE------------LTADDVVFTYSVPLSKdykgergs----------- 121 Bacillus subtilis
YP_845537    106 QVaed---hlTYTFHLRKnIAWAD------GQP------------FTARDIRYSFDRIRDPavdaahlr----------- 153 Syntrophobacter...
NP_662515     70 TMspd---hrSITYILRDdAKWAD------GQP------------ITSRDFKFTYKLYGNPviasprqqflael------ 122 Chlorobium tepi...
YP_344747    151 EVsed---glVFRFHLREgLTFSD------GEP------------LTAEDVAFSFAFIMNPaiaaprer----------- 198 Nitrosococcus o...
YP_001997613  89 TFsdg---gkTATFALRGdAKWED------GKP------------ITSHDLKFSYTLYAEPqvastrqhyindl------ 141 Chloroherpeton ...
NP_662306    102 EFspd---grNVTFHLNSkAVWED------GKP------------LTSKDFSFSYRLYADPnvassrqdylydl------ 154 Chlorobium tepi...
ZP_01857897  176 QSskd---klYDKVVLRDdLTWSD------GTP------------ITAHDIVFTFKTIMNPevpvpavr----------- 223 Planctomyces ma...
ZP_01091691  152 QTsed---gmYDKLVLRDdIYWSD------GKK------------FTAQDVMFSFQVIMDPesrvpavk----------- 199 Blastopirellula...
ZP_04429096  365 QDiqr---etWMTFYLDPrAKWSD------GTP------------FTSTDLKFAFAVLNNNtvdcdavrtyysdltdlda 423 Planctomyces li...
YP_007102    176 ELrtnekglsEYWVFLRQdVFWAPlqqnqfAEGiilaphflrrhpVTAHDFKFYFDAIMNPyveeakavsl--------- 246 Candidatus Prot...
Feature 1                                                               ##                       
1XOC_A       122 ---------------tyemlksVEKKGDYEVLFKlky------------kdgNFYNNAlds-----------------ta 157 Bacillus subtilis
YP_845537    154 --------------nyyqdierLEVLDDHTVRFHyr---------------iPYFLALqfcg---------------gip 189 Syntrophobacter...
NP_662515    123 ---------vgadkgqvdfdraIETPNDTTLIFHfy---------------kPVPEHLalfht--------------slt 164 Chlorobium tepi...
YP_344747    199 --------------ayyekierVTALGPYQVEFKfk---------------ePYFNSLalag---------------gla 234 Nitrosococcus o...
YP_001997613 142 ---------aknadgavdfenaVETPNDTTLILHfs---------------tPLAENIvldhf-------------ydlm 184 Chloroherpeton ...
NP_662306    155 ---------llkpdgsvdfdkaVETPDDKTLVLHfn---------------kPMAENIvldhf-------------ndlm 197 Chlorobium tepi...
ZP_01857897  224 --------------sgtdqirwIEAYDDQTLVFFhk--------------esLPTNVWnln-----------------fp 258 Planctomyces ma...
ZP_01091691  200 --------------qgtdkirwVQAYDDQTVVYFhr--------------esTPVNVWnin-----------------fp 234 Blastopirellula...
ZP_04429096  424 lsplvvrmryrqqyfkafefgaGIGLYTPPFEFFknrlk--------tqttePAITGYeltldrlte------aeedsqk 489 Planctomyces li...
YP_007102    247 -------------riyfgdieeIKILDDYTFIVRwktektvgengkeelkmkYLSKSWtgslcplasfvyqyfadgtkii 313 Candidatus Prot...
Feature 1                                                                                        
1XOC_A       158 iLPKHilgnvpiadl-----eenefnrkkPIGSGPFK---FKEWKQg-QYIKLEANDDYFe-------gRPYLDTVTYKV 221 Bacillus subtilis
YP_845537    190 iVPVHlfkpgedf--------nkhpiarsPVGTGPYR---LLHWRTg-EEIVLVRNEAYWg-------vRPHLDRLVFKI 250 Syntrophobacter...
NP_662515    165 pLPEHlwknvkpee------fresklnqqPVGAGPYR---LADWSKq-QSLTLSSNVSCNlp------kPGNIKRIIYRV 228 Chlorobium tepi...
YP_344747    235 iLAEHfyepylekp------ekfnqskglLLGSGPYRlpdPKGWTPdqGLVELERNPRYWgp------vQPSFDKLLWKV 302 Nitrosococcus o...
YP_001997613 185 pVAKHvfesippee------irsraaelpIVAGGPYR---VEKWSRq-QSLTLVSNETCVlp------hPGKIAKVSFLV 248 Chloroherpeton ...
NP_662306    198 pVAEHlfrdikpqq------irqqaatlpIMGAGPFK---VKEWQRq-SKLVLESNPTSVlp------rPAASPALTFMV 261 Chlorobium tepi...
ZP_01857897  259 iIPKHiyekelesdptlqdspyhvkfenaPVTGGPYE---IEKRERg-QEILLKRRESWYmqdgkqvrtKPYFERVRLRI 334 Planctomyces ma...
ZP_01091691  235 vIPKHvyeetikedptmrlsdahaklesnPICGGAYK---LVKHDRg-QEIVLERREDFYmvdgkqvrrKPYFKTIRFRI 310 Blastopirellula...
ZP_04429096  490 kVSAHgkrfgkffn-------ldtaynqtPLGTGPYM---VESWKKt-DRVILSRNDSYWlp-----erSGYLDKLIFRF 553 Planctomyces li...
YP_007102    314 eEDSHpntyqtnsiwa--qnfshhwaknvIVSCGPWL---FDGMTE--REIRFKRNPDYFna------yAALTEALEFKF 380 Candidatus Prot...
Feature 1                           #                                  #      #                  
1XOC_A       222 ipdanaaeaQLQAGdiNFFNvpatdykt-------------aekfnnlKIVTDLAl---sYVYIGWNekn---------- 275 Bacillus subtilis
YP_845537    251 ipdptvalhVLKQGglDVSGllpiqwvk------------qtqserfqEMFRKLKyytprYNYVGWNmkr---------- 308 Syntrophobacter...
NP_662515    229 ipdytvrlaQLQTGdvDVVEnikpedfa------------avqkanpnVDIKTIGlr--vYDYVGWQnidgayynqtgki 294 Chlorobium tepi...
YP_344747    303 iandsarltTFRNGdiDIYSarpleyqklr---------edqalaartQHFEYRSpa-agYSYIAWNqerng-------- 364 Nitrosococcus o...
YP_001997613 249 ipeyttrltLLKTSklDVLMsagginpkdv--------esltrenpeiTICSVKDr---sFDSIVWLcidgeafrngkki 317 Chloroherpeton ...
NP_662306    262 vpeyttrlaMLKSGqiDALVsagginpkda--------aelaksnpeiAIIPVADryfdsVVWLNIDgeawrngk---ki 330 Chlorobium tepi...
ZP_01857897  335 iedpntallALKNGkiDEMAlnpelwktqt---------edddfyktcTKANGLEw---vYFYFGWNcet---------- 392 Planctomyces ma...
ZP_01091691  311 iedpntamlALKTGsiEEMAitadlwttqa---------nddkfyeknTKVTATEw---vSFHICWNtks---------- 368 Blastopirellula...
ZP_04429096  554 lpdnttalqSLRAGeiDFNYrmdpeqftkd---------lagppdwfkDKFIKADwytpnYGYYCWNlnr---------- 614 Planctomyces li...
YP_007102    381 knspdgiweEFKTDslDLFEippnqlaeldrflqsapyakqkengsgiHRLDYISr---kYYYIGWNqan---------- 447 Candidatus Prot...
Feature 1                                                                                        
1XOC_A       276 ---elFKDKKVRQALTTALDRESIVSQVLdGDGEVay---iPESPlswnypkDIDVPKFEYNEKKAKQMLAEAGWkdtng 349 Bacillus subtilis
YP_845537    309 ---plFADRRVRVAMTMLIDRETILRRVLfGFGTVvs---gTFYVnsp--eyNRNIKPWPYDPAAALALLEQAGWkrrdg 380 Syntrophobacter...
NP_662515    295 rphplFGDPVVRRALTMAIDRQSIIDGYLgEYGVLak---tDISPslk-wayDDSIKPYGYDPAQAVKLLEAAGWmpgpd 370 Chlorobium tepi...
YP_344747    365 -kptrFADRRVRQAMTFLTDRASMIEQIMlGHGEAav---sPFNPdsp--qhDSTLTPRPFDLAKAKTLLAQAGYadrdg 438 Nitrosococcus o...
YP_001997613 318 kpnvfFGDKKVRQAMTYAIDRNSIVDGFM-GEAHAtvv-ntPLSPayk-silDSSLHPYNYNPKKARKLLTEAGWkpgad 394 Chloroherpeton ...
NP_662306    331 kpnrfFGDRRVRQAMTYAIDRQAIIDGFM-GPKHAtiv-ntTLSPayt-siiDTSLPAYAYNPDKALALLKEAGWtpgpd 407 Chlorobium tepi...
ZP_01857897  393 ---lfFKDKEVRQAMSYAFNHKEMLDELCyGLYQPct---gIYHEtaw-mapKPMSKPYTQNLAKAEKLLDDAGWidhdg 465 Planctomyces ma...
ZP_01091691  369 ---pfFSDKRVRQAMSYAFDHQEMIDKLFsGLYEPaa---gPFHPtsw-mspKPMPEPYQQDLDKAEELLDEAGWvdsdf 441 Blastopirellula...
ZP_04429096  615 ---pyFKDQRVRMALAMLFEKEAFLKNKMyNLGTMvsgsqyYFGPg-----yDHSVKSVDYSPETARDLLATAGWidtnr 686 Planctomyces li...
YP_007102    448 ---plFKSKKVRQALTMAIDRERIIRQNLnGMGMQtt---gTFFPfsp--syDATLKPYPYNIQKALELLREDGWydssg 519 Candidatus Prot...
Feature 1                             #                              #      ##           ##      
1XOC_A       350 dg----ildkdgkKFSFTLKTNqgnkVREDIAVVVQEQLKKIGIEVKTQivEWSALVEQMNPpnwdFDAMVMGWSLs-tF 424 Bacillus subtilis
YP_845537    381 ng----plekdgtPFQFEFILPagskIGEQIATMFQENLKQVGIRMEIRklEWAVFIQKIDSr--nFDACTLGWSLg-wE 453 Syntrophobacter...
NP_662515    371 gi-----rqkngrKFSFVLYTNagnaRRNYACTIIQQNLREIGIDCKIEmqESNVFFQNLQDr--kLDAWMAGWSIg-lE 442 Chlorobium tepi...
YP_344747    439 dgv---ledanhqPFRFELVFFqdadDTRRQVLFLKDLYARAGILLEPKptEWSVMLDQISKk--nFDAITLGWTSg-vE 512 Nitrosococcus o...
YP_001997613 395 gi-----lekngqDFSFTLVAPtgnaRRNYAATVVQQNLKDIGIECKLEfaETIVFVQNQNEy--rYAAAMSGLSAe-tL 466 Chloroherpeton ...
NP_662306    408 gi-----lqkngqKFSFELAAPtgnpRRNYAATIIQQNLRKIGIDCRLRfdESLMFNKNQNEy--rYDAALSGLAAe-tL 479 Chlorobium tepi...
ZP_01857897  466 dgirdkefdgkviPFRFSIMTSsq-pLSLSICTLLKENLAQIGVICEVKptEFTVMQEKARNh--qFQAMFGGWGTgtdP 542 Planctomyces ma...
ZP_01091691  442 dgirdkeingkrvRFEFSVTCPps-pIMERVARLLKRSLSKIGVACNIKlvEFTALQQMNLDg--qFEATLGGWGT---S 515 Blastopirellula...
ZP_04429096  687 dg----ildrdgvKLSFEALIPfgnpVIDDRTALLQKTLKQVGVDMQITriEWAAFVERLKAk--dFDLVTLSWAMp-vE 759 Planctomyces li...
YP_007102    520 tgvlekvidgqrtPFKFTLTYFvkspTNKSICEYISTALKEIGIVCKIEgvDVADLSAIVDDk--sFDAIYMAWALgspP 597 Candidatus Prot...
Feature 1             #                                                           # #            
1XOC_A       425 PDQYDIFHSSqik---kglNYVWYKNAEADKLMKDAKsisDRKQYSKEYEQIYQKIAEDQPYTFLYYPnnHMAMPENLEG 501 Bacillus subtilis
YP_845537    454 SDPYQIWHSSmae---kgsNFVGFRNEEADRIIEAARqefDPEKRYRLYHRFGEILHEEQPYTFLFTTetLAAVARRFEN 530 Syntrophobacter...
NP_662515    443 IDPLDVWGSDlkk---srfNFPGFINPRIDQLCELAKnkmRIEDARPYWIEYQKILHEQQPVTFLYWIreTQGFSKRIQG 519 Chlorobium tepi...
YP_344747    513 IDIYQMFHSSqtva--ggdNFIAYQNPELDELIEKARatvDETERMPLWRACERILYEDQPYTFLMRRksLVFVDQRMHN 590 Nitrosococcus o...
YP_001997613 467 PFQLIIWGSNfek---spfNSSAFQNARLDEVIAELGkplGMEKQRELWHEYQQILHDEQPRTFLYYFdeLEGFNRRVKN 543 Chloroherpeton ...
NP_662306    480 PFQLVIWGSDfek---kpfNSSAFQNAELDRVVARLTgplPQTEQAKLWKEYQQILANEQPRTFLYYYdeLEGFNKRVEN 556 Chlorobium tepi...
ZP_01857897  543 DTSINLWKTEaa------rNYVNYSNPEVDKLFEEGRrefDVEKRAKIYGKIHELLYEDQPYTWLYFRnsFYGFNKDLRG 616 Planctomyces ma...
ZP_01091691  516 TDPYSSENIFatg---egrNYGRYSNPEIDKLFDQGQkefDREKRAEIYGEIHKILYEDQVYTWLFYRnsFYGFNKKLRG 592 Blastopirellula...
ZP_04429096  760 SDPFQLWHSSgatpesrgsNAGSFANNLADELIEKIRvtlEPDKRALLNYSLHRLLDAQQPYLFLYCSkdLGAYHKRFRG 839 Planctomyces li...
YP_007102    598 EDPRQLWYSTgake-kgssNLIGFVNQEVDHIIDKLTfeyDVEKRIELYHQFDRIIYDEAPYTFIYTPkeTLLYRDYLQN 676 Candidatus Prot...
Feature 1            
1XOC_A       502 YKYH 505 Bacillus subtilis
YP_845537    531 VKVY 534 Syntrophobacter fumaroxidans MPOB
NP_662515    520 AKLN 523 Chlorobium tepidum TLS
YP_344747    591 LGIT 594 Nitrosococcus oceani ATCC 19707
YP_001997613 544 VNVN 547 Chloroherpeton thalassium ATCC 35110
NP_662306    557 VNLS 560 Chlorobium tepidum TLS
ZP_01857897  617 YVFS 620 Planctomyces maris DSM 8797
ZP_01091691  593 YRFS 596 Blastopirellula marina DSM 3645
ZP_04429096  840 VKWY 843 Planctomyces limnophilus DSM 3776
YP_007102    677 VFIP 680 Candidatus Protochlamydia amoebophila UWE25

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