Conserved Protein Domain Family
PBP1_ribose_binding

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cd06323: PBP1_ribose_binding 
Click on image for an interactive view with Cn3D
Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs
Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Statistics
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PSSM-Id: 107318
View PSSM: cd06323
Aligned: 35 rows
Threshold Bit Score: 287.977
Threshold Setting Gi: 51891911
Created: 2-May-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
ligand bindingdimerization
Conserved site includes 12 residues -Click on image for an interactive view with Cn3D
Feature 1:ligand binding site [chemical binding site]
Evidence:
  • Structure:2DRI; Escherichia coli periplasmic binding protein binds ribose, contacts calculated at 3.5 A
    View structure with Cn3D
  • Citation:PMID 7982928
  • Structure:2IOY_A; Thermoanaerobacter tengcongensis periplasmic binding protein binds ribose, contacts calculated at 3.5 A
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                  # ##                                                                  
1URP_D         3 TIALVVSTLNNPFFVSLKDGAQKEADKlGYNLVVLDsqn----------------------------------------- 41
2FN8_A         4 KMAIVISTLNNPWFVVLAETAKQRAEQlGYEATIFDsqn----------------------------------------- 42
2FN9_A         4 KMAIVISTLNNPWFVVLAETAKQRAEQlGYEATIFDsqn----------------------------------------- 42
2DRI_A         3 TIALVVSTLNNPFFVSLKDGAQKEADKlGYNLVVLDsqn----------------------------------------- 41
gi 15643718   32 KMAIVISTLNNPWFVVLAETAKQRAEQlGYEATIFDsqn----------------------------------------- 70
gi 32472547   49 RVAVIVSTLNNPWFVVLAESARDSAIElGYDAVIFDsqn----------------------------------------- 87
gi 160941558  67 VIGLAMNTQTNPFFVDVKDGVQKAADEhGIELYITDaqd----------------------------------------- 105
gi 14026602   29 LIAIITPSHDNPFFKAEAVGAEAKAKElGYEALVLVhdd----------------------------------------- 67
gi 45440225   33 LIAIITPSHDNPFFKAEAEGAKAKATElGYTTLVAShdd----------------------------------------- 71
gi 51891911   40 ENGAGKSTLMKILGGLYRPEAGEVLID-GRPVTIDSpaaatalgiafihqelnqalhlsvaeniylgrppvtgpfrrvdw 118
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                          #                             
1URP_D        42 ----------------------------npAKELANVQDLTVrGTKILLIN-PTDSDAVGn---AVKMANQ---ANIPVI 86
2FN8_A        43 ----------------------------dtAKESAHFDAIIAaGYDAIIFN-PTDADGSIa---NVKRAKE---AGIPVF 87
2FN9_A        43 ----------------------------dtAKESAHFDAIIAaGYDAIIFN-PTDADGSIa---NVKRAKE---AGIPVF 87
2DRI_A        42 ----------------------------npAKELANVQDLTVrGTKILLIN-PTDSDAVGn---AVKMANQ---ANIPVI 86
gi 15643718   71 ----------------------------dtAKESAHFDAIIAaGYDAIIFN-PTDADGSIa---NVKRAKE---AGIPVF 115
gi 32472547   88 ----------------------------dpSKETAHFDNVIAsGYSAVLFN-PTDADGSIa---NVRRAKE---AGVPVF 132
gi 160941558 106 ----------------------------dpTIQMKDVENLITkKPDAIIID-TCDSDAIVs---SIEACNE---AGIPVF 150
gi 14026602   68 ----------------------------daNKQSQLIDTAIGrGAKAIILD-NAGADATVa---AVQKAKD---AGIPSF 112
gi 45440225   72 ----------------------------dvNKQNQLIETAIArKAKAIILD-NAGSDATIg---PLKKAKA---AGIPAF 116
gi 51891911  119 ramyqgaaavlerlgaqidpratlgslgvgARQMVEIARALSlDARVLIMDePTAALTEPeverLFAVMRSlveAGVAIV 198
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1          ##                                                                            
1URP_D        87 TLDRqat------------------kgeVVSHIASDNvlGGKIAGDYIAkka---------------------------- 120
2FN8_A        88 CVDRgina-----------------rglAVAQIYSDNyyGGVLMGEYFVkflkek-----------------------yp 127
2FN9_A        88 CVDRgina-----------------rglAVAQIYSDNyyGGVLAGEYFVkflkek-----------------------yp 127
2DRI_A        87 TLDRqat------------------kgeVVSHIASDNvlGGKIAGDYIAkka---------------------------- 120
gi 15643718  116 CVDRgina-----------------rglAVAQIYSDNyyGGVLMGEYFVkflkek-----------------------yp 155
gi 32472547  133 CMDReina-----------------tdaAVSQILSDNysGCVAIGQHFVkev---------------------------- 167
gi 160941558 151 TMDRean------------------ggeVISHIGYDAikSGRMAGQYLVdtl---------------------------- 184
gi 14026602  113 LIDReina-----------------tgvAVAQIVSNNyqGAQLGAQEFVklm---------------------------- 147
gi 45440225  117 LIDReine-----------------tgiAVSQIVSNNyqGAQLGAEKFVtlm---------------------------- 151
gi 51891911  199 YISHrleeifticdrvtvlrdgqrigswPIDQVTADHl-ITHMVGRQLTerfpkvevapgdtllevrdlllrgsstpvsf 277
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                         #   #                       #                         #        
1URP_D       121 -gegAKVIELQGIAGtsAARERGEGFQQAvaa-hkFNVLASQPADFDRIKGLNVMQNLLTahpdvqAVFAQNDEMALGAL 198
2FN8_A       128 dakeIPYAELLGILSaqPTWDRSNGFHSVvdqypeFKMVAQQSAEFDRDTAYKVTEQILQahpeikAIWCGNDAMALGAM 207
2FN9_A       128 dakeIPYAELLGILSaqPTWDRSNGFHSVvdqypeFKMVAQQSAEFDRDTAYKVTEQILQahpeikAIWCGNDAMALGAM 207
2DRI_A       121 -gegAKVIELQGIAGtsAARERGEGFQQAvaa-hkFNVLASQPADFDRIKGLNVMQNLLTahpdvqAVFAQNDEMALGAL 198
gi 15643718  156 dakeIPYAELLGILSaqPTWDRSNGFHSVvdqypeFKMVAQQSAEFDRDTAYKVTEQILQahpeikAIWCGNDAMALGAM 235
gi 32472547  168 -gesGEYAELLGLVGdnNTRNRSDGFHSVvdrypeLKMVAQQSADFDRAKALEVMEAILQanpdikAVFCGNDAMAMGAY 246
gi 160941558 185 -ggkGKIVEIQGIMGtnVAQNRSQGFNEVmkdnpdMEIVACQVADFDRAKGMSVMENILQanpeidGLYAANDEMLLGAL 263
gi 14026602  148 -gekGNYVELVGKESdtNAGIRSKGYHDViddypdLKKVAQQSANWSQTEAYSKMESILQanpdikGVISGNDTMAMGAY 226
gi 45440225  152 -ggkGKYIELLGRESdtNAHVRSQGYHDVidehsdMKMVAQQTANWSQTEAFNRMESILQanpditGVISGNDTMALGAE 230
gi 51891911  278 tvrrGEILGIAGLMGa-GRTHRGQGFHEAvdgvqgIDVVASQPADFDRAKGLTVMENILQahpdivAVFAHNDEMALGAL 356
                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
Feature 1                         #                    #                                    
1URP_D       199 RALQTAgk-sdVMVVGFDGtpDGEKAVn-dGKLAATIAQLpDQIGAKGVETADkvlkg--ekvqAKYPVDLKLVV 269
2FN8_A       208 KACEAAgr-tdIYIFGFDGaeDVINAIkegKQIVATIMQFpKLMARLAVEWADqylrg-ersfpEIVPVTVELVT 280
2FN9_A       208 KACEAAgr-tdIYIFGFDGaeDVINAIkegKQIVATIMQFpKLMARLAVEWADqylrg-ersfpEIVPVTVELVT 280
2DRI_A       199 RALQTAgk-sdVMVVGFDGtpDGEKAVn-dGKLAATIAQLpDQIGAKGVETADkvlkg--ekvqAKYPVDLKLVV 269
gi 15643718  236 KACEAAgr-tdIYIFGFDGaeDVINAIkegKQIVATIMQFpKLMARLAVEWADqylrg-ersfpEIVPVTVELVT 308
gi 32472547  247 QALLAAgkaeqVKIFGFDGadDVVAMIq-eGKIVATGMQFpKLMAKTAAEYADqylkg-drdllQKVPVAVELVH 319
gi 160941558 264 EAMEAAgrtdeIVKIGCDAidDTLDAMk-aGKVDATIAEPpFFLGKAILNTAYdyleg--kqvePYVILDNQLVT 335
gi 14026602  227 AALAAAnr-kdVIVVGFDGsnDVRDSIt-sGGIKATVLQPaYAQAQMAVEQANnfiknkkspekEKQLMDCVLVN 299
gi 45440225  231 AALKAAgr-ndVVVVGFDGsdYVRDSIinnGNIKATVLQPgWAQAQMAVVQADqylktgktgleEKQLMDCVLID 304
gi 51891911  357 EAIEAAgkadqIKVVGFDAtdDAVKAVq-eGRMAATVAQKpKEMGRLGVETALkhlng--ekvdEYIPVPLELVT 428

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