1R1N,1MRP,1QVS,1Y4T,2QRY


Conserved Protein Domain Family
PBP2_Fe3_thiamine_like

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cd13518: PBP2_Fe3_thiamine_like 
Click on image for an interactive view with Cn3D
Substrate binding domain of iron and thiamine transporters-like, a member of the type 2 periplasmic binding fold superfamily.
The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. On the other hand, thiamin is an essential cofactor in all living systems. Thiamin diphosphate (ThDP)-dependent enzymes play an important role in carbohydrate and branched-chain amino acid metabolism. Most prokaryotes, plants, and fungi can synthesize thiamin, but it is not synthesized in vertebrates. These periplasmic domains have high affinities for their respective substrates and serve as the primary receptor for transport. After binding iron and thiamine with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The iron- and thiamine-binding proteins belong to the PBPI2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.
Statistics
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PSSM-Id: 270236
Aligned: 22 rows
Threshold Bit Score: 225.643
Created: 4-Jun-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
chemical
Conserved site includes 8 residues -Click on image for an interactive view with Cn3D
Feature 1:chemical substrate binding site [chemical binding site]
Evidence:
  • Structure:2QRY; periplasmic thiamine binding protein from Escherichia coli binds thiamine phosphate, contacts at 4A.
  • Comment:1R1N; tri-nuclear oxo-iron clusters in the ferric binding protein from Neisseria gonorrhoeae, contacts at 4A.
  • Structure:1MRP; ferric-binding protein from Haemophilus influenza binds ferric iron, contacts at 4A.
  • Citation:PMID 9360608
  • Structure:1Y4T; Campylobacter jejuni ferric-binding protein binds ferric iron, contacts at 4A
  • Structure:1QVS; ferric hydroxide clusters in H9a mutant of Haemophilus influenzae ferric ion-binding protein A, contacts at 4A.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                        
1R1N_A         1 DITVYNGqh-----kEAAQAVADAFtra-tgIKVKLNSAk-GDQLAGQIKeegsrsPADVFYSEqiPALATLSAanllep 73  Neisseria gonor...
1MRP_A         1 DITVYNGqh-----kEAATAVAKAFeqe-tgIKVTLNSGk-SEQLAGQLKeegdktPADVFYTEqtATFADLSEagllap 73  Haemophilus inf...
1QVS_A         1 DITVYNGqa-----kEAATAVAKAFeqe-tgIKVTLNSGk-SEQLAGQLKeegdktPADVFYTEqtATFADLSEagllap 73  Haemophilus inf...
1Y4T_A         3 ELNIYSArh-----yNADFEIIKKFeek-tgIKVNHTQAk-ASELIKRLSlegsnsPADIFITAdiSNLTEAKNlgllsp 75  Campylobacter j...
2QRY_A        24 VLTVYTYdsfa-adwGPGPVVKKAFead-cnCELKLVALedGVSLLNRLRxegknsKADVVLGLdnNLLDAASKtglfak 101 Escherichia coli
CAJ48801      28 TLTVYTAle-----aDQIKAYQAAFereypdIKIQWVRDs-TGIITAKLLaeknnpKADVIWGLagTSLGLMDKegmlep 101 Bordetella aviu...
CAJ50964      23 NAICYNCpp----ewADWGTALKAIkek-tgINVPADNKn-SGQALASLAaerknpVADVVYYGvtFGIQAAKDglvqgy 96  Bordetella aviu...
Q57SD5        24 VVTVYSIdglhdgdnSWYQVQFDAFtka-tgITVRYVEGg-GGVVVERLAkertnpQADVLVTAp-PFIQRAAAekllan 100 Salmonella ente...
YP_001322359  40 ELVVYSGrn-----eRFVQALLEKFted-tgIEVLALHG--ANPLQIAEEkn--nvRADIFISNdlGALGYLDSkgllqg 109 Alkaliphilus me...
YP_931448     33 RLVIVGPag----isDLGKELAKKFsek-ygVNATFVPLggAVEMVNELVrnrdnpPWDVTIGVpeFYYMVLIErgvlyc 107 Pyrobaculum isl...
Feature 1                                                                                ##      
1R1N_A        74 lpastinetrgkgvpvaakkDWVALSGRSRVVVYDTrklsekdleks--vlnyatpkwknRIGYVPt----sGAFLEQIV 147 Neisseria gonor...
1MRP_A        74 iseqtiqqtaqkgvplapkkDWIALSGRSRVVVYDHtklsekdmeks--vldyatpkwkgKIGYVSt----sGAFLEQVV 147 Haemophilus inf...
1QVS_A        74 iseqtiqqtaqkgvplapkkDWIALSGRSRVVVYDHtklsekdmeks--vldyatpkwkgKIGYVSt----sGAFLEQVV 147 Haemophilus inf...
1Y4T_A        76 vsskyle-efipahlrdkdkEWFAITKRARIIAYNKntnidiskmkn--yedlakaefkgEIVMRSat---aPYSKTLLA 149 Campylobacter j...
2QRY_A       102 sgvaad---avnvpggwnndTFVPFDYGYFAFVYDKnklknppqsl----kelvesdqnwRVIYQDpr--tsTPGLGLLL 172 Escherichia coli
CAJ48801     102 yapkgldqiapnmrdakpvpAWVGMDAFASAICFNTieakkqnlpvpkswqdltrpeyagKIVMPNpa--ssGTGFLDVS 179 Bordetella aviu...
CAJ50964      97 kpahwd---eiptgmkdpdgKWFAIHSGTLGFMVNVdalngkpipks--wadllkpeyrgMIGYLDpa--saFAGYVGAI 169 Bordetella aviu...
Q57SD5       101 fntd------aasaipdannLYSPLVKNYLSFIYNSkllktapasw----qdlldakfknKLQYSTpg--qaADGMAVML 168 Salmonella ente...
YP_001322359 110 snpegi--etipadfraednAYFAISARARGFIYNKdmiteeempks--nedlfdskwatVENGFAitrggnGGMTGHVS 185 Alkaliphilus me...
YP_931448    108 pgfkve--gvpaeeywdphgCVYPLDKSYIGIVYNEtalaarglkppqtlddllkpeykgLITYPNpv--qsGTGLAVLS 183 Pyrobaculum isl...
Feature 1                                      ###                #  ##                          
1R1N_A       148 AIVKLkgea--aalkWLKGLKEy--GKPYaKNSVALQAVENGeIDAALIN-NYYWHafarek----gvqnvhTRLNfvrh 218 Neisseria gonor...
1MRP_A       148 ALSKMkgdk--valnWLKGLKEn--GKLYaKNSVALQAVENGeVPAALIN-NYYWYnlakek----gvenlkSRLYfvrh 218 Haemophilus inf...
1QVS_A       148 ALSKMkgdk--valnWLKGLKEn--GKLYaKNSVALQAVENGeVPAALIN-NYYWYnlakek----gvenlkSRLYfvrh 218 Haemophilus inf...
1Y4T_A       150 SIIANdgnk--eakaWAKGVLEnlaTNPKgGDRDQARQVFAGeAKFAVMN-TYYIGllknsknpkdvevgnsLGIIfpnq 226 Campylobacter j...
2QRY_A       173 WXQKVygdd---apqAWQKLAKk-tVTVTkGWSEAYGLFLKGeSDLVLSY-TTSPAyhile------ekkdnYAAAnfse 241 Escherichia coli
CAJ48801     180 AWLQLfgee--kgwaYMDALHKn-iGSYThSGSKPCNLAASGeFPIGVSF-DYRAAklka--------dgapIEPIfpse 247 Bordetella aviu...
CAJ50964     170 AVNQAmggsldnfdpGIDWFKKlqaNKPIvPKQTAYARVLSGeIPILIDY-DFNAYrakyk-------dhsnVAFVipae 241 Bordetella aviu...
Q57SD5       169 QAFHSfgskd-agfaYLGKLQAn-nVGPSaSTGKLTALVNKGeIYVANGDlQMNLAqmer---------npnVKIFwpan 237 Salmonella ente...
YP_001322359 186 ALRYQwgdek-taewIAAIRANs--AGIYqGHGDIRRAVGAGeHSFGLVN-NYYFHqqlve------pennnVGFIyldq 255 Alkaliphilus me...
YP_931448    184 WVMSVkgeee-gwryLKQLAGQi--SKIGyPSGFTPLRNALKrGDVLIAL-SWYSHaidp---------gtpNIKAaty- 249 Pyrobaculum isl...
Feature 1                                                          
1R1N_A       219 r--dpgalVTYSGAAVLKssqnkDEAKKFVAFLAGkeGQRALTAVrAEYP 266 Neisseria gonorrhoeae
1MRP_A       219 q--dpgalVSYSGAAVLKasknqAEAQKFVDFLASkkGQEALVAArAEYP 266 Haemophilus influenzae
1QVS_A       219 q--dpgalVSYSGAAVLKasknqAEAQKFVDFLASkkGQEALVAArAEYP 266 Haemophilus influenzae
1Y4T_A       227 d--nrgthINISGIAMTKssknqDAAKKFMEFMLSpeIQKILTDSnYEFP 274 Campylobacter jejuni
2QRY_A       242 -----ghyLQVEVAARTAaskqpELAQKFLQFXVSpaFQNAIPTGnWXYP 286 Escherichia coli
CAJ48801     248 -----glgWEVEATAIVKgtknpEAARKVADFSASraANELYKANfAVLA 292 Bordetella avium 197N
CAJ50964     242 -----gtvVVPYVMSLVKgapdpENARKVLDFTLSdeGQAIWANA-FLRP 285 Bordetella avium 197N
Q57SD5       238 dkgersalAIPYVIGLVQgapqsENGKKLINFLLSkeAQTRVSELsWGMP 287 Salmonella enterica subsp. enterica serovar C...
YP_001322359 256 eedemgvvANAAGVGLVSggpneGNAIAFIEWLLLpeNQVAFVGEsLELL 305 Alkaliphilus metalliredigens QYMF
YP_931448    250 -----safLYREGVAVLKnarnrDLAVEFVKFALSkeGQDLVDPYnYMLP 294 Pyrobaculum islandicum DSM 4184

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