Conserved Protein Domain Family
Periplasmic_Binding_Protein_Type_1

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cd01391: Periplasmic_Binding_Protein_Type_1 
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Type 1 periplasmic binding fold superfamily
Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has six beta strands, while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold.
Statistics
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PSSM-Id: 107248
View PSSM: cd01391
Aligned: 128 rows
Threshold Bit Score: 44.49
Threshold Setting Gi: 46277636
Created: 12-Dec-2003
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1GUD_B          3 EYAVVLktl-snpFWVDMKKGIEDEAkt-------lgVSVDIFAspsegdfqsqlqLFEDLSNk---------nYKGIAF 65
2QH8_A          4 KVAVSQive--hpALDATRQGLLDGLkakgy-eegknLEFDYKTaqgnp--aiavqIARQFVGe---------nPDVLVG 69
gi 548377      28 NIGAVLstr--khEQMFREAVNQANKrhg-----swkIQLNATSvthkp---naiqMALSVCEdlis----sqvYAILVS 93
gi 46277636    38 RLGALMp-----rAPLARARARAALAraalaprlphnLSLELVVaappa--rdpasLTRGLCQalvp---pgvaALLAFP 107
gi 14548162    36 GIAVILvgt--sdEVAIKDAHEKDDFhhl-----svvPRVELVAmnet----dpksIITRICDlmsd----rkiQGVVFA 100
gi 68164778    28 NIGAVLstk--khEQIFREAVNQANKrhg-----twkLQLNATSvthkp---naiqMALSVCEdlis----sqvYAILVS 93
gi 25090493    28 HIGAIFdesakkdDEVFRTAVGDLNQneeilqtekitFSVTFVDgnn------pfqAVQEACElmn------qgILALVS 95
gi 48994235    26 QIGGLFpnqqsqeHAAFRFALSQLTEpp--------kLLPQIDIvnis----dsfeMTYTFCSqfs------kgVYAIFG 87
gi 118092396   25 HIGAIFegnaakdDEVFKQAVSDLNLnddilqsekitYSIKLIEann------pfhAVQEACDlmt------lgILALVT 92
gi 24581733    18 LWIVFInev--dnEPAAKAVEVVLTYlkkn---irygLSVQLDSieank--sdakvLLEAICNkyatsiekkqtPHLILD 90
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1GUD_B         66 aplssvnlv---mpvarawkkGIYLVNLDekidmdnlk-------kaggnveaFVTTDNv-aVGAKGASFIIdklgaegg 134
2QH8_A         70 iatptaq-------alvsatkTIPIVFTAvtdpvgaklvk---qleqpgknvtGLSDLS---PVEQHVELIKeilp-nvk 135
gi 548377      94 hpptpndhftptpvsytagfyRIPVLGLTtrmsiysd--------ksihlsflRTVPPYs-hQSSVWFEMMRvys---wn 161
gi 46277636   108 earpellq-----lhflaaatETPVLSLLrrearaplg------apnpfhlqlHWASPLe-tLLDVLAAVLQaha---we 172
gi 14548162   101 ddtdqeaiaq--ildfisaqtLTPILGIHggssmimad-------kdessmffQFGPSIe-qQASVMLNIMEeyd---wy 167
gi 68164778    94 hppapndhltptpvsytagfyRIPVIGLTtrmsiysd--------ksihlsflRTVPPYs-hQANVWFEMMRvfn---wn 161
gi 25090493    96 sigctsags----lqsladamHIPHLFIQrstagtprsgcgltrsnrnddytlSVRPPVy--LHDVILRVVTeya---wq 166
gi 48994235    88 fyerrtvnm----ltsfcgalHVCFITPSfpve-----------------tsnQFVLQLrpeLQDALISVIEhys---wq 143
gi 118092396   93 stgcasana----lqsltdamHIPHLFVQrstggsprtachlnpsleeeeytlAARPPVr--LNDVMLKLVTelr---wq 163
gi 24581733    91 ttksgiase---tvksftqalGLPTISASygqqgdlrqwr--dldeakqkyllQVMPPAd-iIPEAIRSIVIhmn---it 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1GUD_B        135 EVAIIEGkag---nasGEARRNGATEAfkkas-------------------qiklvASQPAdwdrikaldVATNVLqrnp 192
2QH8_A        136 SIGVVYNpge----anAVSLXELLKLSaakh---------------------giklVEATAlksa-dvqsATQAIAek-- 187
gi 548377     162 HIILLVSddhe-graaQKRLETLLEEReska---------------------ekvlQFDPGtkn----vtALLMEAkel- 214
gi 46277636   173 DVGLALCrt------qDPGGLVTLWTSragr---------------------ppqlVLDLSrrdt--gdaGLRARLapma 223
gi 14548162   168 IFSIVTTyfpg-yqdfVNKIRSTIENSfvgwe-------------------leevlLLDMSldd---gdsKIQNQLkkl- 223
gi 68164778   162 HVILIVSddhe-graaQKKLETLLEEReskskkrnyenldqlsydnkrgpkaekvlQFDPGtkn----vtSLLLEAkel- 235
gi 25090493   167 KFIIFYDse-----ydIRGIQEFLDKVsqqgm-------------------dvalqKVENNink---mitTLFDTMriee 219
gi 48994235   144 KFVYIYDad-----rgLSVLQKVLDTAaeknw-------------------qvtavNILTTtee---gyrVLFQELqkkk 196
gi 118092396  164 KFIVFYDsd-----ydIRGLQGFLDQAsrlgl-------------------dvslqKVDRNisr---vfaNLFTTMktee 216
gi 24581733   162 NAAILYDdsfvmdhkyKSLLQNIQTRHvita----------------------iakDGKREre------eQIEKLRnld- 212
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1GUD_B        193 --------nikAIYCand----tmAMGVAQAVANAgkt--gkVLVVGTdgipeark---mveagqmTATVAQn------- 248
2QH8_A        188 ---------sdVIYAlidntvasaIEGXIVAANQAk------TPVFGAatsyv---------ergaIASLGFd------- 236
gi 548377     215 --------earVIILsas---eddAATVYRAAAMLnmt-gsgYVWLVGereisgn----alryapdGILGLQlingkne- 277
gi 46277636   224 apvggeapvpaAVLLgcd---iarARRVLEAVPPG-------PHWLLGtplppkal---ptaglppGLLALGevarppl- 289
gi 14548162   224 --------qspIILLyct---keeATYIFEVANSVglt-gygYTWIVPslvagdtd--tvpaefptGLISVSydewdyg- 288
gi 68164778   236 --------earVIILsas---eddAATVYRSAAMLnmt-gsgYVWLVGereisgn----alryapdGVIGLQlingkne- 298
gi 25090493   220 lnr-yrdtlrrAILVmnp----atAKSFITEVVETnlv-afdCHWIIIneeindvdvqelvrrsigRLTIIRqtfpipqn 293
gi 48994235   197 --------erlVVVDces----erLNIILSKIIKLekn-gngYHYILAnmgfmdidl-tkfresgaNVTGFQlvnytdtv 262
gi 118092396  217 lnr-yrdtlrrAILLlsp----rgAQTFINEAVETnla-skdSHWVYVneeitdneilelvhsalgRMTVIRqifplskd 290
gi 24581733   213 --------innFFILgtl----qsIRMVLESVKPAyfernfaWHAITQnegei--------ssqrdNATIMFmkpmaytq 272
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1GUD_B        249 -----------------------------pADIGATGLKLmvdaeksgk------------------------------- 268
2QH8_A        237 -----------------------------yYQIGVQTADYvaaileg--------------------------------- 254
gi 548377     278 ------------------------sahisdAVGVVAQAVHellekenitdpprgcvgntniwktg--------------- 318
gi 46277636   290 ------------------------eaaihdIVQLVARALGsatqvqpkrallpapvncgxlqpagpes----------pg 335
gi 14548162   289 -----------------------lparvrdGIAIITTAASdmlsehsfipepksscynthekriy--------------- 330
gi 68164778   299 ------------------------sahisdAVAVVAQAVHdlfekenitdpprgcvgntniwktg--------------- 339
gi 25090493   294 isqrcfrgnhrisstlcdpkdpfaqnmeisNLYIYDTVLLlanafhkkledrkwhsmaslscirknskp--------wqg 365
gi 48994235   263 parimqqwrn---ndarelprvdwkrpkytSALTYDGVRVmaeafqnlrrqridisrrgnagdclanpav------pwgq 333
gi 118092396  291 nnqrcmrnnhrissllcdpqegylqmlqvsNLYLYDSVLMlanafhrkledrkwhsmaslncmrkstkp--------wng 362
gi 24581733   273 yrdrlgl---------lrttynlneepqlsSAFYFDLALRsfltikemlqsgawpkdmeylncddfqggntpqrnldlrd 343
                         410       420       430
                  ....*....|....*....|....*....|....
1GUD_B        269 ----------------vipldkapeFKLv-dSIL 285
2QH8_A        255 ------------------kepgsldVQVakgSDL 270
gi 548377     319 plfkrvlmsskyadgvtgrvefnedGDRk-fANY 351
gi 46277636   336 rflarflantsfqgrtgpvwvtgssQVHm-sRHL 368
gi 14548162   331 -qsnmlnrylinvtfegrnlsfsedGYQm-hPKL 362
gi 68164778   340 plfkrvlmsskysegvtgrvefnedGDRk-fANY 372
gi 25090493   366 grsmletikkggvsgltgelefgenGGNp-nVHF 398
gi 48994235   334 gidiqralqqvrfeglsgnvqfnekGRRt-nYTL 366
gi 118092396  363 grsmletikkghitgltgvmefredGANp-yVQF 395
gi 24581733   344 yftkiteptsygtfdlvtqstqpfnGHSfmkFEM 377
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