Conserved Protein Domain Family
PBP2_NikA_DppA_OppA_like_3

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cd08490: PBP2_NikA_DppA_OppA_like_3 
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 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: 173855
View PSSM: cd08490
Aligned: 66 rows
Threshold Bit Score: 423.553
Threshold Setting Gi: 134099216
Created: 22-Apr-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_616189     41 KVLRVVFnegpdtggsLDPANgwtGWYVHQaGIYETLFYYDa-DMNLMPKLATGYKQlNDTEWEIQLREdVSFHDGTKMN 119 Methanosarcina ...
NP_242662     53 KHIHFLFnvs---tnsLDPHVd-mTYIPVRaGITETLVRVDeeNVTIAPWLAESWDStDGQHWTIKLREdVTFQNGKEMD 128 Bacillus halodu...
YP_001319865  36 KALYTASqya---pdsLDTHKgysGWHTSTyGITETLFKVGd-DFSLEPLLAKKGKA-DGLVWTIVLKDnVNFSNGDLLT 110 Alkaliphilus me...
NP_602468     34 KPIVIGQtfv---vgaIEPTVggtPWSLTThGLSETVFSVDr-DGNLVSRYVEDVERtDKLNWVLKLKKgVKFSDGTEVN 109 Fusobacterium n...
YP_079682     34 KKLTFLFnip---sqtLDPNLd-vNYTAIRaGISETLVKISa-DLSIEPWIAKDWKSkDGQTWVFTLKDnLTFQNGKKAD 108 Bacillus lichen...
YP_001543149  26 GELRIGTginl--ptsLDVAQgsnGYNMLTyGAGETLMRFTp-SNQLEPWLAENVTAlDPTTWQIKLRQgIRFHDGSELK 102 Herpetosiphon a...
YP_173738     33 KELTFLFnfs---sqtIDPHL---DYTPLRaGVTETLVKLNdeELTIEPWLAETWDSeDGQHWTFDIRDdVTFQNGNPLT 106 Bacillus clausi...
NP_782002     49 KKVTYLYvha---tntLNPHLkasGNIPIRtGAVETLVRIDe-DLKLKPWLLEKWNSkDAKHWEFKVRKgIKFHNGTSLD 124 Clostridium tet...
YP_300357     28 KTLNVELplk---ttsIAPYE---TDVPVKiGSAESLFKAGa-NGKVQKLLVDTYNQkSPTQLDLKLKDdIKFQNGKKVT 100 Staphylococcus ...
NP_645028     27 KDLNISLplk---tksIAPYE---TDVPVKiGAAESLFKTNd-QGKIEKALVKSYHQpNDTTLDIELKDnIKFQNGQKLT 99  Staphylococcus ...
NP_616189    120 ADAVLFSLNRVLDptnsrsseysfikeVRKNGEYTIVIETNDVyaPLIASLVDPimsIVSPsivd-adkePIGTGPFKFV 198 Methanosarcina ...
NP_242662    129 AEAVKASLERALDesvaie--nalkidEIEADGYTLHITTKEPfpEFISELVNPnvsIIDVteed-ftnhPVGTGPFALE 205 Bacillus halodu...
YP_001319865 111 ADMVVRNLERVAVenprfs--ymsdfaYEVVNDKTFTITSKKPypTMLNTLANCetgIINLdkttdldnaIIATGPFVVE 188 Alkaliphilus me...
NP_602468    110 AEALAWAMNTVMEenplsna-tagkvkFEKVDDYTVNVAVEREtqNLKSLLTEWt-nIIFKktd----ngYIFTGPYVIK 183 Fusobacterium n...
YP_079682    109 AKAVKASLERTMReskamk--nalkikEIKAEGQTLTITTKEPfpEFPSELVHPntsIIDVsaan-isqqPVGTGPFQVS 185 Bacillus lichen...
YP_001543149 103 ASDVLNSFNSSWQnlsgaknfipadtnVNVVDDYTLTLTTSQAegSIPYSLANWn-fVIHKpav---ngiSILTGMYQPI 178 Herpetosiphon a...
YP_173738    107 AESVKKSIERAMEvnpgvs--evlnidYMEANELELTIVTNEPfpQFPSELVHPnasIIDVdgad-pekkPIGTGPFKID 183 Bacillus clausi...
NP_782002    125 ANIVKANIEACIKnnpgik--nalnieSMEAKEDILKIVTKKPnaSLPSEFVHPntaIIDVnasd-idtkPCGTGAFKVE 201 Clostridium tet...
YP_300357    101 GQAVKASLEESIKksdlvk--gslpikEIKVDGQNVSITTKEAypELVSELASPfsaIYDTkadsdvtkaPVGTGPYQIK 178 Staphylococcus ...
NP_645028    100 AEKVKSSLENSMKksdlvk--yslpisSITAKGQKLTIKTNSAypELVSELANPfmaIYDTdaksdvnqtPVGTGPYQIK 177 Staphylococcus ...
NP_616189    199 SFEPsTSLEIEKNPDYWGgDVKVDRILIQYNKDstaRTLMIKSGDVDIARdplqsdysa-lqanpdinVISRETLRTYFL 277 Methanosarcina ...
NP_242662    206 SFTPgSKLELVRYDEYWDgASKLDSVTFSFNEDasaRSLALESGQADIVYrpevesiet-lqanegimVEATETFRTHNL 284 Bacillus halodu...
YP_001319865 189 KFIPqTTTTLSRNENYWNgDVILDKAIFYRMSDedtLLMAMQNGEIDGYTgvnaaamevfkadpetykLVTVPATRVQLY 268 Alkaliphilus me...
NP_602468    184 NLEPeVSLTLEPNQYYEN-SEKRGEVIIKAISDmasMKLAYESGELDMAFgitpeiag--elkdegkiVETIDAGYQYFG 260 Fusobacterium n...
YP_079682    186 SFEAgHKIELERYDDYWDgKPKLKHVTFSFNEDanaRVMALQSKDADIIYrpsvedidq-iqkdssitVDSVPSLRVHQI 264 Bacillus lichen...
YP_001543149 179 SLEKdQELVLERFANYWDgQAGLQKISVKKIPDanaRALALQSGDLDLLTnvspdiar---glpadieIQSVAGTRMHYV 255 Herpetosiphon a...
YP_173738    184 TFVAnSSLNVERFDDYWDaGAKLDRASFTFNEDesaRLSALKSRGADIVYrppvdslve-lnedpeykTESVVGLRTHEL 262 Bacillus clausi...
NP_782002    202 NFKHnSSIQLVKNDKYWDgEVKVDKVNFEFNQDanaRLQALQSGYADIIFkpaaesiet-lkkdskvtIDTMPGLRTNEL 280 Clostridium tet...
YP_300357    179 DYKQsQNIKLDQFKDYWQgKPKLDHVNVTYQEDgnaRSSDLSSGKADVITdvpvekekt-lnqgdkttTSSVSGFRTSLI 257 Staphylococcus ...
NP_645028    178 DYKQsRKISLSNFKDYWQgKPKLDHITVTYQEDgnnRVRNLESQKDDLITdvpvnkvqd-iennqnlkVSKESGFRTSLL 256 Staphylococcus ...
NP_616189    278 FVNggkaPFDDVRVRQALSYAINRQEIVDTALeGVSGIpatgiftntmpwnakdqieayeYNPEKALELFEEAGItkgtd 357 Methanosarcina ...
NP_242662    285 TMNldrdSLKDVNVRRAVDVLLDRQEIVDTIMlGYAEVadgpfiptlp---fapsyekkeTGTDIAIQYLEEAGYtleng 361 Bacillus halodu...
YP_001319865 269 FLNq---NRLNANVRKAINLTIDANEIVSFLG-GTVSAtvgpfssss----aygkvhkpsVDTDAAVSLLEKDGYvrnge 340 Alkaliphilus me...
NP_602468    261 VLNteagIMSDKSVREAVSLGLDREDYIKALKgGRVANglfaqyfp------fagdvkveYNLEKANSILEENGWklnkd 334 Fusobacterium n...
YP_079682    265 LYNtkkdHLADRHLRRAFDALLNRKEIAESILnGHAQPadgpfladfp---fssdtvqkpSGLQAAKAELKKAGYeleng 341 Bacillus lichen...
YP_001543149 256 MLDsahpPFDDRLVRQAMALAIERQALLQATLdGQGAVatnlypatv----gielveaqiFDPAQAASLLDQAGWvvgsd 331 Herpetosiphon a...
YP_173738    263 VFNtqkeVFADANVRNAFDALIDREELMDDIMsGQAELaegpflpefn---ftpayevkeTGKEVALAWFEKAGFdiene 339 Bacillus clausi...
NP_782002    281 LYNikkpLTGNEYFRKGLDSLINRKEIVENIMsAQATIaygpfmeglp---faidykknqFGLDKALENFKKAGLtvtdg 357 Clostridium tet...
YP_300357    258 MYNht-sKKMTKPVREALDKVVDRESIAKNVSkNHATPatgpfntkld---fidkqqvqkQDIDEAKKIMAAQGYtka-- 331 Staphylococcus ...
NP_645028    257 MYNht-nKKMTKSVREALDHIIDRQGIADHIYqGYAKPatspfndkip---yikepkltkQNIEQAKTLLAKDGYtke-- 330 Staphylococcus ...
NP_616189    358 gklyyngepfTIEIQTYtkraaLQPSAEILASQLEDIGIISTVTildSSALTANAVAg-tYDFSLAAWstapTGDPDYFL 436 Methanosarcina ...
NP_242662    362 qm-qkdgeplHFTVLTYgsraeLPLIAQVFQSNAKQIGIEVEIRq--IEVPEEYMASnrdWDLITYSNvtspRGDAGYYL 438 Bacillus halodu...
YP_001319865 341 gyfekdgkilEVNIAYYpa-rsLDVLATLMQEQLKNIGIQAVLTs--YENPDSTYIAtsdFDIALYSMnadlSGDPEYFI 417 Alkaliphilus me...
NP_602468    335 glrekdgkilSINILTYnsrpdLKIIMQVMLSQLNKMGIEAKTSi--VDNIDVEAKKk-eFDLILYAQhtapTGNPAYFL 411 Fusobacterium n...
YP_079682    342 ka-vkdgkalSFTLLTYqsrpeLPLIAQILESNAKELGISIKIQq--VENIDEYLAKnddWDLATYSSmtapRGDASYLL 418 Bacillus lichen...
YP_001543149 332 gmrskdgqplAFTLHSYpgraeLTLMAIAIQAQLQTLGIKVEVNe--VADIGEVLEKg-nFQASMYSIg--tSGDPQYTV 406 Herpetosiphon a...
YP_173738    340 mv-tkdgeplELKLVTYtsraeFPILSQALQSRAKEIGIEISIEv--LENYEDYLIEeedWDLGMYSPliapRGDASYFL 416 Bacillus clausi...
NP_782002    358 kv-ldngkpiKLKVVTYasraeLPPIAQLVQSNAKKIGIEMNISiveGENVDNHLKSd-dWDFCVYSLltapRGDAGYYL 435 Clostridium tet...
YP_300357    332 -------hplKLTVSTYngrpeLPKMAQVLQSDAKKANIDITIRn--VDDIEGYLKDksqWDASMYSFgtipRGDTGYFF 402 Staphylococcus ...
NP_645028    331 -------hplKIKLITYdgrpeLSKIAQVLQSDAKKANIEIDIKs--VDDIEGYLKDrsaWDATMYSFgtipRGDTGYFF 401 Staphylococcus ...
NP_616189    437 SLHYLSTGNyaanwlRYSNPQVDELILEARketDEERRAELYDEIQIQIQEdAAILPVFYAneIYALSS-DVEGFv-mYP 514 Methanosarcina ...
NP_242662    439 NATYHPTGAln--fsSVNDPELTGIIDELNrtvDQDVRAKLTEQAAAYIDEqKIHSFLIHPsaVVAYDEnKVKNWv-tTR 515 Bacillus halodu...
YP_001319865 418 TNTLKDGAFyn--vgGFKSAECEKLIAELGsemNTVKRAELANEIIQIAIDdDAYGYVVIFnkVTVLRS-GVSGYaesSP 494 Alkaliphilus me...
NP_602468    412 NQFFRTDGSkn--mmSYSSKEVDELLDKMGtipYGDELIKTAKQIQEIIYKdLPVLYLVDPewNVALSE-RLKDYk-pYG 487 Fusobacterium n...
YP_079682    419 NTAYMPNGAln--ysGIENQTLIKWIKEFNrtiDKEKRNRLAKKAAELIEKeTLNSFIVTPenITAYRD-GVLNWe-tSK 494 Bacillus lichen...
YP_001543149 407 GITLVEDAAyn--yaGYKNPAIESAFAELRaeqDPIKRIAIAKRIQTEVKNdPTNLYLASPplISAYRKgSISGYv-pNP 483 Herpetosiphon a...
YP_173738    417 NVSFKPEGAln--fsKVDDPELTSLIEELDgtiAEDERNKLIEQALLHIDKkTYYSYLVHPniVVAYND-RVSNWt-tSK 492 Bacillus clausi...
NP_782002    436 NSSIKPEGSln--hgYINDDKLTAIINEFNsciDETKRNELAKQATTIINKkNYNSYVAYPnvIVAYNNqRISNWk-tSP 512 Clostridium tet...
YP_300357    403 NQAYKPEGAin--agGYDNAKVTKLIDQFNktvDKTERNRLTNEIIDITDKdKANSYLTYMdnIVGMNK-KVKNLk-aTP 478 Staphylococcus ...
NP_645028    402 NQAYKKDGAin--kgDYNNSNVDDLINQLNhtvDVKERHNISNDIIKLSSRdVPNSYIAYNdqIVAANA-KVKNYk-vTP 477 Staphylococcus ...
NP_616189    515 NEYT 518 Methanosarcina acetivorans C2A
NP_242662    516 SEYY 519 Bacillus halodurans C-125
YP_001319865 495 FDFY 498 Alkaliphilus metalliredigens QYMF
NP_602468    488 GDYY 491 Fusobacterium nucleatum subsp. nucleatum ATCC 25586
YP_079682    495 SEYY 498 Bacillus licheniformis ATCC 14580
YP_001543149 484 NDVY 487 Herpetosiphon aurantiacus ATCC 23779
YP_173738    493 SEYY 496 Bacillus clausii KSM-K16
NP_782002    513 SEFY 516 Clostridium tetani E88
YP_300357    479 EGIY 482 Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305
NP_645028    478 EGIY 481 Staphylococcus aureus subsp. aureus MW2
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