2D5W


Conserved Protein Domain Family
PBP2_thermophilic_Hb8_like

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cd08513: PBP2_thermophilic_Hb8_like 
Click on image for an interactive view with Cn3D
The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like import systems, contains the type 2 periplasmic binding fold.
This family includes the substrate-binding domain of an ABC-type oligopeptide-binding protein Hb8 from Thermus thermophilius and its closest homologs from other bacteria. The structural topology of this substrate-binding domain is similar to those of DppA from Escherichia coli and OppA from Salmonella typhimurium, and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. 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. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporters and chemotaxis systems. Members of the PBP2 superfamily function in uptake of a variety of metabolites in bacteria such as amino acids, carbohydrate, ions, and polyamines. Ligands are then transported across the cytoplasmic membrane energized by ATP hydrolysis or electrochemical ion gradient. 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: 173878
View PSSM: cd08513
Aligned: 68 rows
Threshold Bit Score: 273.005
Threshold Setting Gi: 225016663
Created: 29-May-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
peptide bindingdimer interface
Conserved site includes 7 residues -Click on image for an interactive view with Cn3D
Feature 1:peptide binding site [polypeptide binding site]
Evidence:
  • Structure:2D5W_A; Oligopeptide binding protein from Thermus thermophilus HB8 binds a pentapeptide, contacts at 4 A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                      #                                                 
2D5W_A         7 SLVIGAsq-ePRVLAGDFLRvisn--qaiKSEIEqy--lFAPFIGFNa------dSQNFPV--LATEVPTlengrlrvtd 73  Thermus thermop...
YP_002760545  33 VLTIATpadaDALIPPIVASlqg----kqAVDLL-----FDMLARPTgaietvgdAGFAPQ--LASRWSWaad------- 94  Gemmatimonas au...
YP_002761555  27 TVVMASgs-dLESGNPLVTIh-------pLSRQLqrhalFVTLVRLD--------SALQPVpyAAQRWRWdtd------- 83  Gemmatimonas au...
YP_002522011  74 TFREGIig-rIETLNPLLAEsta---eaaVSVLV-----FEGLVWVD--------GSGVPQpaLAERWTMsdd------- 129 Thermomicrobium...
YP_001430471  44 EGVVGA----PLHLNPLLVDpaadpvaadLHRLI-----FEGLTRPGp------dGLPMPA--LAESWTVdds------- 99  Roseiflexus cas...
YP_001635931  44 EAVVGS----PITPIPLLNDpvadpvgrtLISLL-----FEGLTRIGs------dGLIEPA--LAEGYTVdat------- 99  Chloroflexus au...
YP_001634768  98 SIRIAAp---VTDLRPWQPRsrg---eehLISLL-----YSGLMRLD--------ADLWPNpdLAERLDIdvd------- 151 Chloroflexus au...
YP_001275296  71 NLTIRLsd-dSGTLQPWHPRtr------gEEQIIgl--iYSGLMRLD--------ATLAPQpdLATGWVAsad------- 126 Roseiflexus sp....
YP_001546778  41 TLTIRTaq-dIAALHPWKPTch------eEAQLLgl--lYRGLTKLD--------QSLAPQpdVATSWQSdsi------- 96  Herpetosiphon a...
YP_002760273  42 TLIVAVpa-ePATLFPPLAEgs------qDAAIIga--vFDRLAEIGpaletygdGGFRPR--LASSWVWagd------- 103 Gemmatimonas au...
Feature 1                                                                                        
2D5W_A        74 igggkkrlEMDITIRPdAKWSDGRPITTEDVAFYFEVGKAkgmp---vlnpDFWERv---nVRIKD---ARNFTLIFEPa 144 Thermus thermop...
YP_002760545  95 ------slSIAFTIDSaARWHDGQPVGASDVVFSYALYTDssvas--phagAFAGId---sVTARD---ASTAVVWWSRr 160 Gemmatimonas au...
YP_002761555  84 ------qqAVEFSLAPgLRWHDGVPTTAADVAFTLDAAADsal-----gspRRGDVgivrhVAVLD---SLTVRVEFTAp 149 Gemmatimonas au...
YP_002522011 130 ------glEYTFFLRPdAQWHDGEPVTARDVLFTIRLLQDprfprnetmanFWRTVt----VEVVD---AESVRFRLPEp 196 Thermomicrobium...
YP_001430471 100 ------gtVYTFTLRSgVAWHDGAPVTVDDVLFTMRAVQGpa-------faGDQNVaafwrTVLVDragERSVSFRLDSp 166 Roseiflexus cas...
YP_001635931 100 ------geIYTFNLRPgLRWHDGTPITADDVVFTFRTLQTldva----gepALAGFwrtalIERVD---TRTVRVTLSGp 166 Chloroflexus au...
YP_001634768 152 ------grRLTFTLRQnVYWHDGEPLTAADVLFTLEALRSlpets-tallaDLRYIa---aASAPD---ERTVVIELRSr 218 Chloroflexus au...
YP_001275296 127 ------grVITFTLRSdAVWHDGRPVTVDDVVFTLDALRAlppst--allaGLRRIv---eVTAPE---SDTIVIRLDEr 192 Roseiflexus sp....
YP_001546778  97 ------gqTLTMTLRSdIRWHDDTTLTAADAAWTISAMQSisptt--plltDLQGLvr--kVTAPD---DTTLVISLREp 163 Herpetosiphon a...
YP_002760273 104 ------slSIAFTIDSlARWHDGQPVVANDVRYTFQVYTSdsvaa--snrsMLGNId---sVSVRD---PRTAVFWFKRr 169 Gemmatimonas au...
Feature 1                                                                                        
2D5W_A       145 y---yYDTYGp--iNTYAPKHimgpewervkaaargldpdkdaeklnelyrnfflkfatpqalnrgaMVYSGPFKLKRWV 219 Thermus thermop...
YP_002760545 161 hpeqfFQVAYn---LAIMPAHllssvprga----------------------------laqsefarhPIGSGRYRFGAWT 209 Gemmatimonas au...
YP_002761555 150 q---sVLPVVfa-eLPLVPRHlldsvprar----------------------------wrghafataPVGNGPFRFVSRT 197 Gemmatimonas au...
YP_002522011 197 -----YAPFPtylsLPILPEHvlagtvvsd----------------------------llrsrfesqPIGSGPYRVVRVD 243 Thermomicrobium...
YP_001430471 167 -----FAPFLrltgFPILPAHllrdtppeq----------------------------weamafnrlPVGAGPYRLIERD 213 Roseiflexus cas...
YP_001635931 167 -----FAPFPslarVPILPAHllrglspae----------------------------wpasefarrLVGSGPFRLAELR 213 Chloroflexus au...
YP_001634768 219 -----YAPMLsllaVPILPRHlfagrdvs-------------------------------qinfldqPIGSGPFRLRERQ 262 Chloroflexus au...
YP_001275296 193 -----YAPIFslltTPVLPRHlligrnla-------------------------------efnawdvPFGSGPFRFEQRE 236 Roseiflexus sp....
YP_001546778 164 -----YAPLLsalsMPILPKHvfeqlspve----------------------------ldqlnlltqPIGSGPFMFEQRT 210 Herpetosiphon a...
YP_002760273 170 tp-qqFHDATy--hMYVLPSHllagtsmkq----------------------------laaspfarnPVGSGRFRFGSWV 218 Gemmatimonas au...
Feature 1                                                                                        
2D5W_A       220 Pg-NSIEMERNPNFPikpeggeSKYVQKVVYRFiqntNSLLVAVIGGs---IDATSsvsltfdqgrspqlvrrapgrfDI 295 Thermus thermop...
YP_002760545 210 Rs-QMLVFEADTNNYr-----gAPGIARVIWNVtpdaTAASLRVLSGe---ADLLEa--------------------iRL 260 Gemmatimonas au...
YP_002761555 198 Pg-RRWEFARNTEFPtal--ggPPQLQRLVVAVvdeaATKFAGLVSGe---IDLAGvspama----------hlvardSL 261 Gemmatimonas au...
YP_002522011 244 RdrGVIELARHESYRr-----pTPLFERVELHFfesvDEALAAFRRGd---LDAVDlvpwg------------algdpKL 303 Thermomicrobium...
YP_001430471 214 D--QHALLRANSSYFg-----sPPFIETIELRFfrteQDALAALTRGd---IQGLAflst--------------galaDV 269 Roseiflexus cas...
YP_001635931 214 S--DAAILTANPTYYn-----gRPFLDQIELRFvstaEAAIAALSRGe---VNGFAerw-----------------gtNL 266 Chloroflexus au...
YP_001634768 263 Ad-GSLVLERHDQYHh-----gSPLLDQVMLTVmpetATAQQALRDGqllvAELPWgaqd---------------alvDV 321 Chloroflexus au...
YP_001275296 237 Pg-VAITLAANQAFYr-----gAPLLDRVVFVIapdaQVAASALQDErlllAELPWsvgsvi-----------tetspML 299 Roseiflexus sp....
YP_001546778 211 Ag-SAISLIRNSNYId-----gVPYLDRVAFVVapdpQVARQAVRDGdllaAELPWaq------------------sqGL 266 Herpetosiphon a...
YP_002760273 219 Ag-QRVEIVADTSNPr-----gRAKLDRVIWSIasdfGAATVKLFAGe---ADFFEyir-----------------qgDL 272 Gemmatimonas au...
Feature 1                                                                                        
2D5W_A       296 W---------FVPGa---------iWEHIDINkfencq-vvkdlgLNDKRTRQAILHALNREGLVKAFFd-----GLQPV 351 Thermus thermop...
YP_002760545 261 Daya---qaaATKGlalvp-yhtldYAYLAFNfsarsa--atqqlFADHAFRVALSASLDRQALVQNVLge---lGLVAL 331 Gemmatimonas au...
YP_002761555 262 Lt-------lMTPPvl--------fSQVLAFNttr--------apFDDARVREALSLSIDRVRLVQAAVag---yGVPAA 315 Gemmatimonas au...
YP_002522011 304 MgsrvriyapLLAG-----------YTALFLNsqa--------qfFADVRVRQALSLAIDRVQLVRDVLnnwaepGNGPI 364 Thermomicrobium...
YP_001430471 270 N---------LPRNvvrrq-alldaCTVLTFNlrd--------gpLTEIGVRRALAMALDKDALIAGVLn-----GQVAR 326 Roseiflexus cas...
YP_001635931 267 At-------iDLPGeeqqivlpmdeYTLLTFNlrl--------plFQDIPLRRALALGLDRDALIETVVn-----GMAQP 326 Chloroflexus au...
YP_001634768 322 Tt--------LRNGsip-----engVYFLAFNlrp-------grpFADVRLRQALATAIDLPRLVETATk-----GVGVP 376 Chloroflexus au...
YP_001275296 300 Qwg-----ayAENG-----------YYFLAFNlrs-------driFSDPRLREALAATIDLPRIVQEVTd-----GQGML 351 Roseiflexus sp....
YP_001546778 267 Gptvg-igsyPENG-----------FYYLAFNmrd-------griFSDQRVRQALALSLDLNTIVETAGp----aAQAIL 323 Herpetosiphon a...
YP_002760273 273 Gqi------aRAPSlrlvd-nralqYFFLGFNlndasgsaaphpiFGNVQVRRALHMAVDRASIVRNAYds---lGLVAL 342 Gemmatimonas au...
Feature 1                                                                             #          
2D5W_A       352 ahtwiapvnp---lfnpnvkkyeFDLKKAEALLAEMGWrkgpdgilqrtvnGRTVRFEIEYVttagnvvRERTQQFFAED 428 Thermus thermop...
YP_002760545 332 gpftravpa-----adtavaqiaYDTTAADRTLDSLGWsrgang--lrsrsGTPLRFEVIVPass--atRQRMATLMQAQ 402 Gemmatimonas au...
YP_002761555 316 gaippglpfssnaaaatdtaarrQQLTRADALLDASGWrrvgtg-gtrqrqGSPFTITLLTVgs----gDMAVEQLVQAD 390 Gemmatimonas au...
YP_002522011 365 ppasway----------qaqeyrFDRAAALSLLREAGWedrngd-gvldkeGLTFRFTLLTNvdd--pqRVAVAQAVAQQ 431 Thermomicrobium...
YP_001430471 327 ldtpilhgww---aeapdvqwyePDPARAVSALDALGYvagadg--irarnGQRLAFTLLTDss---pkRRAVAEEIARQ 398 Roseiflexus cas...
YP_001635931 327 idtpllpgtw---addpalrrmpAEPSVAAERLAEIDFepgddg--irqrgRQRLSFTLLVDrd---erRVAVAEAIAAQ 398 Chloroflexus au...
YP_001634768 377 vgngalpgsw----adltpplpaGDLPAAREILDAAGWvlppga-tirqreGVPLIARLYVRndd--erRLVAARRIAEI 449 Chloroflexus au...
YP_001275296 352 igssaapgsw---adltpppagtVDLDRARALLDEAGWrlppeg-airqrdGVPLTVQLFVRadd--prRVRAAELIASA 425 Roseiflexus sp....
YP_001546778 324 sdhlpgtwv------aptgelpkRNLDQARELLDQAGWvlpega-tirasnGITLSMALFVRgdd--qrRIEVAERIAAA 394 Herpetosiphon a...
YP_002760273 343 gpapralip-----dttsfkqlpYDPTAARAMLDSAGWldtnnd-gvrerdGRRLSFELLVPnss--agRRSLAILLQEQ 414 Gemmatimonas au...
Feature 1                               #                  ###          #                        
2D5W_A       429 LKKIGIAVKINna-----pSAVVFADEFIqraseckwtGMFEFAWvsn-lqEDGSLFqyknlntgai-------mvptke 495 Thermus thermop...
YP_002760545 403 FRARGVDMRIAai-----ePAQFFARVGSgd------fDAALNMWh-----ADPSPMavrdvwg-------------spr 453 Gemmatimonas au...
YP_002761555 391 LAERGITVNIRvmelatflATVRAADKAGqa-----ayDMAVTGVp-----GDIALGhlsamfa--------------sa 446 Gemmatimonas au...
YP_002522011 432 LAEIGISVTVQp------vASATLQRQLLnr-----eyTAAVFGWms--ltGDPDMFefwhs-----------------s 481 Thermomicrobium...
YP_001430471 399 WSAIGVRIVIEq------vESGDLQRRLEth-----dfTMALHGWqr--lgSDPDVFelwhs-----------------s 448 Roseiflexus cas...
YP_001635931 399 WRSIGVEVFVEs------vDVTTLTERLRqg-----dfMAAIHTWtr--igPDPDPYslwhs-----------------s 448 Chloroflexus au...
YP_001634768 450 AASIGIQIVVEpa----dfATVILARYVApy-----dfDLLLGSWln--gaGDPNFAdtmfydpddfalfhssqleqgpg 518 Chloroflexus au...
YP_001275296 426 AEQIGMDIVVQpa----dfATVIRSKYAPpy-----dfDLLIGSWvn--gvADPDFAdyafydpddfalfhssqinqgla 494 Roseiflexus sp....
YP_001546778 395 TRPVGFNIVVTpa----dfESVIRSKLVTpf-----dfDLALMSWgnsrvgGSPSYTaydpdnfslfhss--qiyqgvad 463 Herpetosiphon a...
YP_002760273 415 LRAVGAEVKPLv------lEVSAFSTRTDgr-----kfDAYMGGWa-----SSPGLVgmpqt-----------------w 461 Gemmatimonas au...
Feature 1                                                                                     
2D5W_A       496 nnyqGQNIGGWrNDEFDRLTSQAvlefDPERRKQLFWRAQEIWAEeLPALPLYFRa---nPYVVRK------GLVNY 563 Thermus thermophilus
YP_002760545 454 gndvGGNFGRYrNTTVDAAFDTAattfDPTRRRTLFHRAFAELVRdVPAIWLYEPr---nMALMRE------RVRPT 521 Gemmatimonas auran...
YP_002761555 447 qrggALDYTGFhDDGLDRALASArt-aSAVDAAVAWRVVDSTLQAsMPVAWLYHAr---gVQGRSR------RLHHV 513 Gemmatimonas auran...
YP_002522011 482 qaeeGANITGFrSRTIDVLLEKArqvsDQDERRSLYVEFQRLFAEyVPAIVLYYPr---yCFVMSD------RIGGV 549 Thermomicrobium ro...
YP_001430471 449 qaerGRNYTGLtDADIDELLYNArkiyDIADRAALYNEFQQRWVDlAPGIMLYQPf---lIHATVA------DLGSI 516 Roseiflexus casten...
YP_001635931 449 qaddGLNYAGLeDSRIDTLLEQAraepELIARAEFYHAFQQRWLElSPAITLYQPm---yVMVTTA------NLQGR 516 Chloroflexus auran...
YP_001634768 519 dtraTRNFVGFnDPVYDEQALIArqlyGREERRSAIAQTQARLASeLPYLYLWVDrtavvINTRVQ------TLDGP 589 Chloroflexus auran...
YP_001275296 495 dtrpTLNFVGFsDPIYDNQAGAArqlyDLSERAQAIQRAQERVALlRPYLFLWADr----IAVVCNp-----RVKTP 562 Roseiflexus sp. RS-1
YP_001546778 464 grpgLRNYGAFqNTSFDNLSTAAralyATERRRELYQQTNTIIQTeYPYVFLWADri--pVALAKQv----rSTQGE 534 Herpetosiphon aura...
YP_002760273 462 gakgSGNVGRYrSMAFDALVDSAlttfNREASHRYWARAFQQIVNdAPAIWLAEQra--pVALHKRfivpplRPDGW 536 Gemmatimonas auran...

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