1ZLQ,1UIU,2NOO


Conserved Protein Domain Family
PBP2_NikA

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cd08489: PBP2_NikA 
Click on image for an interactive view with Cn3D
The substrate-binding component of an ABC-type nickel import system contains the type 2 periplasmic binding fold.
This family represents the periplasmic substrate-binding domain of nickel transport system, which functions in the import of nickel and in the control of chemotactic response away from nickel. The ATP-binding cassette (ABC) type nickel transport system is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, the initial nickel receptor. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA. 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: 173854
View PSSM: cd08489
Aligned: 38 rows
Threshold Bit Score: 521.402
Threshold Setting Gi: 70725148
Created: 21-Apr-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
substrate
Conserved site includes 8 residues -Click on image for an interactive view with Cn3D
Feature 1:substrate binding site [chemical binding site]
Evidence:
  • Structure:1ZLQ_A; Escherichia coli nickel transporter (NikA) binds FeEDTA(H2O)- , contacts at 4 A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                           #         #                                                 
1ZLQ_A        5 EITTAWpvn---vgpLNPHLYtp-----nQMFAQSM--VYEPLVKYQaDGSVIPWLAKSWTHSEDGKTWTFTLRDdVKFS 74  Escherichia coli
NP_618342    53 SITIMVsg------kLNPEDAspie-sstEMCLYEM--VYEPLVKYGkDGVIEPGLAESWNISDDGTQYTFYLRKdVKFS 123 Methanosarcina a...
YP_252062    29 NITVSLptea-kadkLDAQGYd------aAMPVYSA--VYDALVKYDkDKGVKAGLAEKWHVDESGKVYEFHLKKnVKFS 99  Staphylococcus h...
YP_519061    47 NLPESWgfes-fypvLTPANSss-----gYGITYYLtsFYDTLVTYDdKGELAGLLAEEWSVSPDGKVYTFKLREgVKFS 120 Desulfitobacteri...
YP_555215    23 TLTVALaqea-gkldLLQNES--------ALSSYGL--VFDGLVHYGqGGKLEPDLAESWNVSPDGKIITFQLRKdVRFS 91  Burkholderia xen...
ZP_02036959  45 ILTTAVsaelntlypLNMDVQ--------NNIGTKL--CYEGLVNYE-NGEVVPCLAESWEFSDDGTALTFHLKEgVTFH 113 Bacteroides capi...
ZP_02037787  48 NLAESWgfey-fytiITPEVSss-----sYDITYYLtsFYDTLFEYNsEGEVVGVLAEDWSMSEDGMVYTFQIKQgVKFS 121 Bacteroides capi...
ZP_03759427  45 ILTTAVgaelntlypLNMDVQ--------NNIGTKL--CYEGLVNYE-IGDIVPCLAESWEFSDDGTALTFHLKEgVTFH 113 Clostridium aspa...
ZP_03781032  40 KVITALvs-----sdLKPEEAdtisgineDFRLFEM--VFDPLVRYGeGGEIEPALAESWEISEDGKSYTFHLRKdVKFS 112 Blautia hydrogen...
ZP_04060504  20 EVKVSLaref-npsqLDAQAFd------vPMPVYSA--IYQPLVTYGeNGKIEPGLAKSWKVSNNGKDYTFHLKHhIKFN 90  Staphylococcus h...
Feature 1                             #  #                                      #               
1ZLQ_A       75 NGEPFDAEAAAENFRAVLDNrqRHAWlelan--qivdVKALSKTELQITLKsAYYPFLQELALPRPFRFIAPsqfknhe- 151 Escherichia coli
NP_618342   124 DGTGFNADSVVSSAKRWDPT--RFSTpl-------tnVEKLDDYTVRLTFKeNSYPVLIELTYPRPFRSASEnsfdan-- 192 Methanosarcina a...
YP_252062   100 DGSALDAKAVKFSIERAKAMn-KDTTvetlk--kldkVVVKSDHVVQIRLKsPSNQVLNELTQVRPLRIMSPhsvengk- 175 Staphylococcus h...
YP_519061   121 DGTPLTAEDAAQSLLAVPVNlgQYNGgygklstiiadAVAKDDYTLELHLTqPYYSTLRDLCLANPFAIVSSeqlngdlt 200 Desulfitobacteri...
YP_555215    92 DGTPFDANVAQWNMARWIGKp-DFSWisvse--nferMEVTGPYTLRLFLKaPAPVALAELSIVRPVRFLSPkavdak-- 166 Burkholderia xen...
ZP_02036959 114 DGTPFNAEAVKTDFEFAHPNp-NFSNisava--kvesIEVVDEYTVTFHYPnAYFAYLMDFCYPETMVLVSPavleegn- 189 Bacteroides capi...
ZP_02037787 122 DGSDLTAEDVAKSILAVPVNlgQYNGsygrlstiiedAVATDEYTVELHLTqPYYNTLRELCLANPFGIVSSeqfnddlt 201 Bacteroides capi...
ZP_03759427 114 DGTPFNAEAVKTDFEFAHPNp-NFSNisava--klesIEVVDEYTVTFHYPnAYFAYLMDFCYPETMVLVSPavleegn- 189 Clostridium aspa...
ZP_03781032 113 DGTKFNADNVIFNASRWDEKq-TFSAkl-------ldVKKVDDYTVTFEFDqVAYPCLIEFTYPRPYRMLGEngvdee-- 182 Blautia hydrogen...
ZP_04060504  91 DGSNFDAKAVKFSIERAKATdkTNPMetld---klksVTIKDNYTVDIHLKmPSNQVLNELSQIRPLRIMSPhavkdgk- 166 Staphylococcus h...
Feature 1                                                                                       
1ZLQ_A      152 --tmngikaPIGTGPWILQESKLnQYDVFVRNENYWGEKPAIKKITFNVIPDpttRAVAFETGDIDLLYGnegl-lplDT 228 Escherichia coli
NP_618342   193 ----gnfikMIGTGEWMVESYVPeEEVVMVPNPYYYGTKPDIKKITIRKVTDgesRIMALQAGEADLSLAdl----paES 264 Methanosarcina a...
YP_252062   176 --vngkfekAIGTGAFVVDKTGK-EKTTMKPNKYFNHSHPVNYNLAFQTIEDgdsRNSAVQSGSVDISGGalgm-lsdQQ 251 Staphylococcus h...
YP_519061   201 -akdsfttvSYGTGPYMYGGDGDgKKYTFVRNPHYWGEQPDVDSFTIKVIADndaKVLALKNGELDFMSGiak--vssES 277 Desulfitobacteri...
YP_555215   167 ----gqqtsPVGTGPWKILQNDR-SETVLVPNDYYWGKKSSIKRINLSVVPDelsRANALRSGDLDIIGGewvapllpAR 241 Burkholderia xen...
ZP_02036959 190 ---yqsmngVVGTGPYVYEEIVDgDYVRFVRNENYWGEQPYYDEVIVKYIPDasaRLQALQSGEIDLIYGsal--ltwDD 264 Bacteroides capi...
ZP_02037787 202 akqesfrsaTYGTGPYMYAGDNDgQTWNFIRNPNYWGEAPEVDSFSIKYIPDndaKILAMQNGEVDFLSGikn--vsaES 279 Bacteroides capi...
ZP_03759427 190 ---yqsmngVVGTGPYVYEEIVDgDYVRFVRNENYWGEQPYYDEVIVKYIPDasaRLQALQSGEIDLIYGsal--ltwDD 264 Clostridium aspa...
ZP_03781032 183 ----gnfkeMIGTGQWMIESYKTnQEVVLVPNPNYYADAPKVDKVVLKLVDDgqaRTMALQSGEVDICLAdl----ptES 254 Blautia hydrogen...
ZP_04060504 167 --ttgkfekAIGTGPFKVADSTN-ETVTFKPNPYYHNHHPLDYDLIFQTIEDsdsRHLAMESHSIDITGGsl----ghLT 239 Staphylococcus h...
Feature 1                                                                                       
1ZLQ_A      229 FARFSqn---paYHTQLSQPi-eTVMLALNtakaptnELAVREALNYAVNKKSLIDNALy-GTQQVADTLFapsv-pyaN 302 Escherichia coli
NP_618342   265 KSIIEss---knLAVKTAEGt-mGFFLMLNqenealqDKNVRLALNYAIDKDSIVENILg-GDGVAAKGILpetvpyvtD 339 Methanosarcina a...
YP_252062   252 IKQDKkn----kNLTVEDKPstvSHFMAFNpdndvlkQRTIREAISKSIDTKDIAGKSVn-GLFQKNVQFVn-------K 319 Staphylococcus h...
YP_519061   278 YQEMKnt---kgFGAAVDKAptqTYYLGYNlknplfaEQVVREAMAAAIDKGNIVEGIFg-GIHEQADTFFaqsl-pycD 352 Desulfitobacteri...
YP_555215   242 AKALStd---teVGVFAAPGv-sTVLLGFNdtrgpltDVNVRRAINLGIDRTSIAKILYq-GYADPASNLFppti-pdaG 315 Burkholderia xen...
ZP_02036959 265 YQQALsl---pnIAGAVAESdskTRNLVLNasg-vlsDLKVREAVAYAIDKETLSEGLTy-GEETPADHLFpdgi-pytD 338 Bacteroides capi...
ZP_02037787 280 YAQMEqt---dgYGAQVDEKslqTYYVGYNlsseifgDQVVREAISSAIDKDAVVDNIYg-GLFDKADTFFsrdl-pycD 354 Bacteroides capi...
ZP_03759427 265 YQQATsl---pnIAGAVAESdskTRNLVLNasg-vlsDLKVREAVAYAIDKETLSEGLTy-GEETPADHLFpdgi-pytD 338 Clostridium aspa...
ZP_03781032 255 WPVIEqd---enLEEFEAHAt-qTYYLILNyeneflkDEKVRQALNYGIDKNGLVNDLLd-GDGTPAKGLFpdntpyvtD 329 Blautia hydrogen...
ZP_04060504 240 PQQIKesyrnqdLKVKQYPSt-eTQFMAFNpevsllqNKKMREAISKAINTDHLSSNKQlkGLFQDGVEFVn-------D 311 Staphylococcus h...
Feature 1                                                                                       
1ZLQ_A      303 LGLKPSQ-YDPQKAKALLEKAGWtlpagkdIREKNGQPLRIELSFIgtd-alsKSMAEIIQADMRQIGADVSLIGEEESS 380 Escherichia coli
NP_618342   340 ENSEGYS-YNPEKARELLAESGYtdsngdgIVEKDGVPLSLKLVFQseeyaswKSMCEYMQAAAREVGIDIQLEQRDTSA 418 Methanosarcina a...
YP_252062   320 DNQQAHD-YDVKEAEKLLKEAGYhkn-sdgIFEKTGKPLTFNLVIQtaefpswKDKAEKVQRQLKKAGIKLNVKTLDSQS 397 Staphylococcus h...
YP_519061   353 VEQTTYE-FDLAKANRLLDDAGYvdrdgdgIREINGTRLAAEFVYQtes-vanNDMVVYLCDQFKKIGVELTPKSAPMME 430 Desulfitobacteri...
YP_555215   316 KREPVIV-RDVATANKILDAAGWvka--gaVRRKDGKDLALNLLASdqvlpgsRRLSELLLGQLADLGITVTVSSLDDAT 392 Burkholderia xen...
ZP_02036959 339 VELNVVRtYDPEKANALLDEAGWmmnestgIREKDGQALSLKYTYDsgd-alnKSLATAIKSQLAAVGINVETEGQEMMT 417 Bacteroides capi...
ZP_02037787 355 VEQTVYG-FDLDHANQILDEAGYvdtdgdgIREKDGVKLSAAFLYQtgt-asdDNMVVYICDQASKIGIELTPQSAQMMD 432 Bacteroides capi...
ZP_03759427 339 VELNVIRtYDPEKANALLDEAGWvinestgIREKDGQALSLKYTYDsgd-alnKSLATAVKSQLAAVGINVETEGQEMMT 417 Clostridium aspa...
ZP_03781032 330 ENSPGYT-YEPEKAKELLKEAGYedtdgdgIVEKGGKKLSLRLVFQteeyanwKTICEYLQSEYEKIGVEIELNQMESAA 408 Blautia hydrogen...
ZP_04060504 312 TNQHTHS-YNPTQATRLLEQLGYkkn-drgYFEKNGRDLSLKLALQtdefpewKTKAEIMQQDLKNVGIHLDINVLDAQT 389 Staphylococcus h...
Feature 1                         #   #                                                         
1ZLQ_A      381 IYARQRDGR-FGMIFHRTWGaPYDPHAFLSSMRvp-sHADFQAQqgladKPLIDKEIGEVLAthDETQRQALYRDILTRL 458 Escherichia coli
NP_618342   419 YYDAIWKNRdFDMIIYRTYEdSWNPHGFLRSMFy---QTEGSTSvc-wyDPQLNTYLDEVIKtqDETTRQAKYDRIFELI 494 Methanosarcina a...
YP_252062   398 YYDTLWTKKdYDLIFYRTYSdALMPYNFMSSVFk---NNDGKSGvl-anDKTLTQQLDDFPTtvSKKEQQRSFDEIFKHF 473 Staphylococcus h...
YP_519061   431 WYAMITGGQ-YGVTVFKTQGgYYDPANIVSAMNps-qSMDPIIMqaggfLPDGVNLINEVNSttDEARIEEIYATILNTI 508 Desulfitobacteri...
YP_555215   393 YHDRRQKFD-YDLAFFTTYAaPYDPQGSLSAMFv--sTADSGPDgkifvSKDLDAVVQTALSa-AGDDRKEKVQKIYDWM 468 Burkholderia xen...
ZP_02036959 418 WWQEGVAGN-YDLIMWNTEQpYTSPHNYFIPMLsrspHVPSLTAve--gSDKFLALIEEFQTtdDPTRVQEIFDQLLNFD 494 Bacteroides capi...
ZP_02037787 433 WYAMIQSGD-YGLTIFKTQGgYYDPAMVITNINps-tSMDPILMqigasQPELAALVDELDSatDEARIQEIYNTILTTM 510 Bacteroides capi...
ZP_03759427 418 WWQEGVAGN-YDLIMWNTEQpYTSPHNYFIPMLsrspHVPSLPAve--gSDEFLALIEEFQTtdDSARVQEIFDQLLNFD 494 Clostridium aspa...
ZP_03781032 409 YYDAIWSTRdYDMIMYRSYEdSWNPHGFLSSMFy---QTEGNPAvc-wyDEQISTQIGQVLQtlDENKRTELYDSILGRM 484 Blautia hydrogen...
ZP_04060504 390 YYETLTIRKdYDLIFYRSYTnALMPYNFLNARFk--qDGDKPGMfa--nDVQLTTMLNRFSTitNKDDQQRAFNHISHRI 465 Staphylococcus h...
Feature 1                                         #    
1ZLQ_A      459 HDEAVYLPISYIsmMVVSKP-ELGNIPYApi--aTEIPF 494 Escherichia coli
NP_618342   495 NDEALVVPLCYPnkQYAYNT-RLQNVTVApt--nYEGIE 530 Methanosarcina acetivorans C2A
YP_252062   474 NQQYYGVPIAYPneTFVVSD-KVKQFKFSg---lTDAPI 508 Staphylococcus haemolyticus JCSC1435
YP_519061   509 ADNCLMTPLYYThqVALYND-KVAGYDFP-----GDASF 541 Desulfitobacterium hafniense Y51
YP_555215   469 DKNAAICPLVYPqrLWAYNK-RVDGFALPpt--eYDMPI 504 Burkholderia xenovorans LB400
ZP_02036959 495 NDNVLDLPLLFVkdMIVYNTdKVAGYDFSstpmfFDVRL 533 Bacteroides capillosus ATCC 29799
ZP_02037787 511 ADQCLTTPLIYTrqLAIYSD-AVASYTFP-----TDASF 543 Bacteroides capillosus ATCC 29799
ZP_03759427 495 NDNVLDLPLLFVkdMIVYNTdKIAGYDFSstpmfFDVRL 533 Clostridium asparagiforme DSM 15981
ZP_03781032 485 DEQAVTVPLYYPrkVYVYNKnRLTGIEEAst--sYEAIH 521 Blautia hydrogenotrophica DSM 10507
ZP_04060504 466 NQQYLEVPIAYPneVFVTSP-KIKQFEFSg---qTDAPI 500 Staphylococcus hominis SK119

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