Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_9

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cd08496: PBP2_NikA_DppA_OppA_like_9 
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 can bind 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: 173861
View PSSM: cd08496
Aligned: 15 rows
Threshold Bit Score: 462.963
Threshold Setting Gi: 220911201
Created: 8-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:
NP_946796     43 ILKVAApan--psSLDPATgga---gsDHSILwt-iYDTLVEWDydtLKPKPG-LAKWSYPdp---nTMVLDISEgIKFH 112 Rhodopseudomona...
YP_002486510  41 TLTIGVesdsasfGYDPIRva----daQRQFMeg-lYDTLLDLQp-dGTAGPG-LATKFDYnad-stVLTLTLKDgVTFT 112 Arthrobacter ch...
CAJ88238      35 TLNIATmtf--pqSLDPAQav----gsALPYFqa-tYDTLVKREp-dGELRPM-LATEWQYnad-rtELGLTLRKdAKFA 104 Streptomyces am...
YP_002766690  60 ELKVATshv--paSLDPCAgni---gyDIDYLql-mYAPLIDAEpatQKLRPG-IASEWGFsgpdnlTFEMTLQNgLTFH 132 Rhodococcus ery...
YP_001504797  44 TLTLAMsad--itGWDPSNqpgy-qgwGPEAI----WDTLIKCDa-fGKPEAD-IADKWTVsad-gkSFTAHIREgQKFS 113 Frankia sp. EAN...
YP_001504819  49 TLSLAIqat--pnSFDPAElt----sgQSSFVwsalYDTLIWKDn-kGKLQPN-AAESWNYsdg-grTLTLKLRKgMSFS 119 Frankia sp. EAN...
YP_002486864  42 ALTLGTlrd--ltSWDPAQahvghalqPYQAA----YDSLILREp-dGKLSPM-LATAWKYnda-rtKLTVDLRTdVTFS 112 Arthrobacter ch...
ZP_01131609   45 SLTFGYfep--atSLDPQQgts---sqDLPWLlp-vYESLFAYNe-dGSIGLG-LLDEYEQtd---qSLTMHLRDgLTFQ 113 marine actinoba...
YP_998166     50 VLRIASpan--psSLDPAVgga---gsDHAILwt-mYDTLVEWDy--ATLKPKpGMAEWIFpd--pkTMLLRIKPgISFH 119 Verminephrobact...
YP_715552     24 TVHWGTkqi--pvAWDPVVtgs---taATNYLtp-iYESLFTLNe-kREVKPA-LAEGYSYnqa-gdQITIRLKPkLTFQ 94  Frankia alni AC...
NP_946796    113 DGTSLDAEAVKFNLDRNRSdqrsnvkp----dlssvdsVEVTG---PLQVTLKLknpDTALPAil-sdRAGMMVSPTNIk 184 Rhodopseudomona...
YP_002486510 113 DGSTLDAALVKANFDRRTDtalstysaiakggaqeiasVDVVS---PTQVAITFakpQPGFEKnl-tsTMGMIVGKTGVa 188 Arthrobacter ch...
CAJ88238     105 DGTVFDAAAVKANMERFKTgggadak-----wlkdlesVAVDD---PTHVTLKLrqpNPAMLFyl-sdAAGLMANPAAFd 175 Streptomyces am...
YP_002766690 133 DGTTLDAAAVKASMEHCLSlgivsv--------ptiksVEATS---PDQIKISLsapTSGLPGwl-ngRLGMIVSPTALt 200 Rhodococcus ery...
YP_001504797 114 DGTPVDSAAIAASFQYLTShggsqg-------dykglkTDAPD---AQNITLTWpepQPMIIQr----VCNPKITTKALl 179 Frankia sp. EAN...
YP_001504819 120 SGAPVNAVAVKTTLERSKNtpgftdq-----vlgalesVDAPD---DRTVVLRLshpDGALLDslavsGAGVIGDPATLn 191 Frankia sp. EAN...
YP_002486864 113 DGAKFDAEAAKANLDHFKKangpqma-----qlstvsdVAVVD---ADTVDINLsapEPALEFfl-sqAAGLMGSPKALg 183 Arthrobacter ch...
ZP_01131609  114 DGTSLDADAVVANIERGQTletssvks----dlasissVEAVD---DLTVELTLsegDAALPAkl-adRAGMIISPAAIe 185 marine actinoba...
YP_998166    120 DGTPCDAEAVRWNIERNRGdaasnl-------kadlssIEASAvvsPTQVKLMLdqpDAALPAvf-sdRAGMMVSPTAQk 191 Verminephrobact...
YP_715552     95 DGTPVNAEAVKFNIERIKTqqnsalkg----synnvrsATVID---DLTVRLDLgqqDYQIPYll-svRGGMLPSKAAAq 166 Frankia alni AC...
NP_946796    185 algn-dtdrKPVGAGPWKFVRWNDn--EIVVVARNENYWRk--gRPFLDGIEFNIIpenatalRSVVAGQnDMAFqlpar 259 Rhodopseudomona...
YP_002486510 189 dta--slatTPDGSGPYTLDPSTVk-gNKYVMVKNEKNDDa--aDYAYSKIVFNVImdpqaraNALVSGQaDVAQltspt 263 Arthrobacter ch...
CAJ88238     176 kgd--glktTPDGTGPYRLDRTKTtvgTKWVYQRNPDYWGe---PLPYETLTMSFFdnetaivNGLKTGQvNAALlqsad 250 Streptomyces am...
YP_002766690 201 aagt-dfanKPVGAGPYTFTSAVPn--SSYTFSRFDDYKPagppNPQLAKIQIQVIsnptaltNALTSNAaDFAYgltps 277 Rhodococcus ery...
YP_001504797 180 dsg--kvndKPVGSGPYVLDETATtrgSVYTFTKNESHWNt--aAYPYKKLVLKVIesetarvSALKTGQvDGSLitaas 255 Frankia sp. EAN...
YP_001504819 192 dkr---talNPVGSGPYVLNTGQTvngSTYVLDRREDYWNv--qAYPFKTVKISVIrdrtaalNALQAGEvNAGTvevtn 266 Frankia sp. EAN...
YP_002486864 184 tda---iktEPVGSGPYVMDKAASvkdSQTVFNAREGYWNk--dLQKYKKLTLKILldptartNALVSGQiDATLldpkn 258 Arthrobacter ch...
ZP_01131609  186 dgt--nlaiNPIGAGAWKLVEYAPg--DSLQLERFDGYWNp--dAVKLQDLTIRLIddddtrlNAIRAGEvDIAQitaaq 259 marine actinoba...
YP_998166    192 aagk-afgrNPVGAGPWRFVSWADn--QKVIVTRHAQYWRt--gLPYLDGIEFSIIpelatglRSVVSRQnDLAYqlsar 266 Verminephrobact...
YP_715552    167 adpvklsqtNPVGAGPYKVVEIVPe--SKIVLEKWDGYWDa--aNIHVKRIEINFGidantlvPGLQSGVyNFAQidgsq 242 Frankia alni AC...
NP_946796    260 lkpvierakdlKLV--SSPTl--yCIQVYFNyara----pldNIKVRQAINFALDRDTFVKAALs-GLGEParMTLPSSH 330 Rhodopseudomona...
YP_002486510 264 vd--fakskgvGVSr-IGGTv---QTMVSFDktgkt-apafaSEKVRQAIQYAINRQALVDALHk-GDIPTw-NALPKDS 334 Arthrobacter ch...
CAJ88238     251 qq--isiesdpRMKt-TEQEfd-fQGLLLFDrggkl-tpalkDARVRQALNLAIDRKTMLEAIRq-NRGEItsQVFGPDT 324 Streptomyces am...
YP_002766690 278 sapilernpnlNVS--HDPRl--gVALVVINnknp----vvnDVRVRLAMQYALDRKAIARAALdsAEGTAafGQYPPGS 349 Rhodococcus ery...
YP_001504797 256 yn--eveasglNVVt-MQGQ----TTRLLLTdhlgkevpalgSLKVRQAINMVFDRDAMVKNLYq-GHGKPayQIFRPGS 327 Frankia sp. EAN...
YP_001504819 267 vd--rlraagfDAAv-VEAHs--lASLVLADrtges-lkplgDPRVRQAINMAFDREKIVEQLLr-GSGKPteQVFNPKD 339 Frankia sp. EAN...
YP_002486864 259 g----kqaegaKMK--LEANqvdwAGLLLLDrdgak-npalaDVKVRQAINYAFDRKTILDQVMl-GQGTPtsQPFGKDS 330 Arthrobacter ch...
ZP_01131609  260 ve---lasadsDLTvrTDPSl--aVDHIGLNigtp----pfdDPLVREAINYAIDREALLEGLYr-GNGIVawQPFPPGY 329 marine actinoba...
YP_998166    267 yrpiitrekalRLV--TGPTl--yCIQLYMNyara----pldNPKLRQAINFALNREAFVKATMd-GVGEPahMNLPSTH 337 Verminephrobact...
YP_715552    243 iq--qargaglDILagVNRQw--gSTFLSLNinka----pftDPKVVEAIRYAVNPAEFATKLGf-GEGEPshQPFPKGH 313 Frankia alni AC...
NP_946796    331 wAYAKDVagtYPYDPEKAKKLLAEAGYkdglEMTIGGYtdq--dsVRRGEVIQDQLGKVGIKLKFTrg----tIAEISAQ 404 Rhodopseudomona...
YP_002486510 335 aGFTADLektFAYNPEKAKSLLAEAGYp--nGFEFTIIaga--qtQTDLQAVQKDLAAVGITMNVK-------MAASTDE 403 Arthrobacter ch...
CAJ88238     325 hGYDRKLdtyYAHDPARAKELLRTAGHa--eGFTLKLPriaaivnDALAASLASDLEAVGVKLVWDdl----dGASAVQK 398 Streptomyces am...
YP_002766690 350 qFYDEETedaWPYDPEKAKSLLAEAGYp--nGVTVRGLagnlppySTNAVLVGEQWEKVGIKVDFVem----sGPQAITE 423 Rhodococcus ery...
YP_001504797 328 dAYIDGMadpYPFDVTKAKALMAEAGYa--sGFDLSLPtmagqnhETLMPYVTQQLGLLGIKVKQVpl----sGANAIGD 401 Frankia sp. EAN...
YP_001504819 340 pAYDPALnttYAYDPQRAKRLLAEAGYp--nGFSVTMPeff--laKSFAPTITQSLAAIGITTTWEpvppqqtDAAISSK 415 Frankia sp. EAN...
YP_002486864 331 gAWSEELenyYSYDPEKAKQLLKESGFe--gKVSIDVPtlp--gaETLISVLKQQLADVGITLNPGaaitntfTADVAAQ 406 Arthrobacter ch...
ZP_01131609  330 fANDPSLenaFPYDPEKAKELLADAGYp--dGFTFDLKtnnqafrVQSSEAIAGMLADVGITANIIpl----eGPTILDE 403 marine actinoba...
YP_998166    338 wAYDKSVaglYPHDVAKARQLMADAGLa--aGIDLTIGgytdqdaVRRGEIVMDQLGKIGIRLKFTng----tIPEISGQ 411 Verminephrobact...
YP_715552    314 pAYVGALdseHPYDPARAREILAKAGYad-gAISFEIAgla-nnfDQVAEVLQEQLKAVGIRTTIKlt----dFANWSKG 387 Frankia alni AC...
NP_946796    405 FFAqek--kfdMLVSAWtgrp------------dpsmTYGLGFdkgayy----nagrtaDPELSKLIQESRAs-qDLNER 465 Rhodopseudomona...
YP_002486510 404 AFAavattplgYAPLGWdnpig-----------lmygAILNGFtnvq---------katDDQLSAATGEAAAa-kDDAAR 462 Arthrobacter ch...
CAJ88238     399 VFTd-------RAYSGMvmnmgqsssdwvvvdelvnpGAFNMFgt-------------sDATVRELVPRVQSg--TAEQA 456 Streptomyces am...
YP_002766690 424 FVAhns---adVFSVGWpt----------------raSAPLNFeaslgsrsyfrqnsvpNEELEKLIALLNNt-yDESAQ 483 Rhodococcus ery...
YP_001504797 402 LLSg------tYPVVLWqlgnfgqsll-didvvvrstGYWNLEhq-------------pDATVDGLWEKILTg--DEATR 459 Frankia sp. EAN...
YP_001504819 416 KYPa------fFLIAGLett---------------agDASRYFskdgaf----npfhaeDPDLTPQVEQATQt-iDPRQA 469 Frankia sp. EAN...
YP_002486864 407 KYSa-------MYFNLFqgeptvai-----dqivstkALYNPFkt-------------tTPELEDKIKAVRT---AGDAA 458 Arthrobacter ch...
ZP_01131609  404 FYYq-------LTVPAYftpwgg--------radpsqTLDNLFsptgln----npakiaNRELTDLLDEARAs-tDQDAR 463 marine actinoba...
YP_998166    412 FFGtek--kfdMLLSAWtgrp------------dpsmSYSLMYakgayyn---agrsefSPELSALLQESRAr-eDIQWR 473 Verminephrobact...
YP_715552    388 YYGk------tLAASIFgyvgr----------dshvqALTEHYdtggvln---lsspytSAPFQQALKAVRAtpiDSPDY 448 Frankia alni AC...
NP_946796    466 AAVFAKIQRFTVEqALSAPLAFQyeLDALSA---KVKDF 501 Rhodopseudomonas palustris CGA009
YP_002486510 463 KTALTKMNTRLVEsGWLIPLFESlsNWGYNTk--KVQEV 499 Arthrobacter chlorophenolicus A6
CAJ88238     457 GAAVRALGEHLVKeAWFVPFYRMt-YLHVSDgsvTIRPQ 494 Streptomyces ambofaciens ATCC 23877
YP_002766690 484 LDIVKQINQVVIKsAEYVPLYFTpdVVAYTK---NVHGA 519 Rhodococcus erythropolis PR4
YP_001504797 460 KTAQQDINRYVIEqAWFAPMVNPdgFYAHSPd-vKIDHV 497 Frankia sp. EAN1pec
YP_001504819 470 ADAYRHVNATAVRdAWNAPLFYVa-VHWVTKk--GITYL 505 Frankia sp. EAN1pec
YP_002486864 459 GEEAKEVNKYVVEqAWFAPLFRVnqMYYHND---KVNVV 494 Arthrobacter chlorophenolicus A6
ZP_01131609  464 GALFREASANIMEeSRMIPLMFPgvTFAIRS---NVIGY 499 marine actinobacterium PHSC20C1
YP_998166    474 KSVFAKIQRMVMEnALVAPLAFQfeIDALSN---AVQGF 509 Verminephrobacter eiseniae EF01-2
YP_715552    449 PSRLQAAAKAGYEnGSTVSLYTYasAIAKKK---SLSDL 484 Frankia alni ACN14a
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