Conserved Protein Domain Family
PBP1_AmiC_like

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cd06331: PBP1_AmiC_like 
Click on image for an interactive view with Cn3D
Type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF)
This group includes the type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF), found in bacteria and Archaea. AmiC controls expression of the amidase operon by a ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon is induced. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems.
Statistics
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PSSM-Id: 107326
View PSSM: cd06331
Aligned: 97 rows
Threshold Bit Score: 252.459
Threshold Setting Gi: 54022536
Created: 2-Feb-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
ligand binding
Conserved site includes 5 residues -Click on image for an interactive view with Cn3D
Feature 1:ligand binding site [chemical binding site]
Evidence:
  • Structure:1QNL_A; Pseudomonas aeruginosa AmiC binds butyramide, contacts calculated at 3.5 A.
    View structure with Cn3D
  • Structure:1PEA_A; Pseudomonas aeruginosa AmiC binds acetamide, contacts calculated at 3.5 A.
    View structure with Cn3D
  • Citation:PMID 7813419

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                   #    
1QO0_A         9 LIGLLFSETGvtadIERSQRYGALLAVEQLNReggvgGRPIETLSQDPgg-dpDRYRLCAEDFIRnrGVRFLVGCYmSHT 87
1QNL_A         9 LIGLLFSETGvtadIERSQRYGALLAVEQLNReggvgGRPIETLSQDPgg-dpDRYRLCAEDFIRnrGVRFLVGCYmSHT 87
gi 27377955   10 KVGMIAEETGalsfMGRANANVARMVVDEINAnggllGRKIELYLEDGat-tdAVAEAKAAKLVLqdKVDVIFGGIySST 88
gi 13471873    7 KIGLVAELTGplsfMGVANANLTTMLVDDINAkggllGRPVELVIEDGet-tdSAAKAKAAKLVDvdKVDVVVGGIySST 85
gi 37677088   31 KIGAVLPLTGtfavYGEQAVRGAELAVEQINAkggvlGRPLELVIRDNatdpaKTVKYSRELILNe-DVFALLGPVsSSS 109
gi 89093139   28 KIGVVLPLTGpfeiYGQQGLNGALLAVEDINQrggvlGHPIELVVRDNqt-dpALSVRLSRELIQieDVFALLGPVsSAA 106
gi 27375307   45 KVGIATDLTGpiayAGNADANVAKMVIKEINAaggmlGRPLELYIEDTas-neSVAVGNVRKLIQrdKVDMVLGGItSSM 123
gi 91781258   52 KLGLATDITGaisyAGGADANVARLLVKQINAaggllGRPIELYIEDTas-neTIAVANTRKLIQrdKVDIVIGGVtSAT 130
gi 109645894 271 KVGIIGDFTGicseLERGKVAAYKLAADEINRmgginEKKVELLFRDDrs-lsELTREAVKELTEeeRVDVLMGSTlSPS 349
gi 120612457  35 KIGLLTPFSGplarVAEANRNCLMMAVDEINAaggllGQALQIVSEDSqm-saKVSLDKARKLLAgdGVAMVTGMVlPFE 113
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                         #  ##                                          #               
1QO0_A        88 RKAVMPVVEr-ADALLCYPTPYEGfeyspnivYGGPAPNQNSAPLAAYLIrhy-geRVVFIGSDYi-yPRESNHVMRHLY 164
1QNL_A        88 RKAVMPVVEr-ADALLCYPNPYEGfeyspnivYGGPAPNQNSAPLAAYLIrhy-geRVVFIGSDYi-yPRESNHVMRHLY 164
gi 27377955   89 RQAIKGPAVvkGRTLYIYPEQYEGqecdplifCTGPVPAQQLDPLIPWLMhktgarTFYLPSADYi-wPHVMNERVRRLV 167
gi 13471873   86 RLAIKSEAVtrGKTLYIYTEQYEGqendplifCTGPVPAQQVEPLIPWLMnstgakRFYLPSADYi-wPHLLNKAASRAV 164
gi 37677088  110 RYAMSEIATe-LRTPMFYGIDYEGrhyspyliCYSTIPEHYIAPIVPYLAenv-gsSFYIFGYDYi-wPHRMSQRIVEEV 186
gi 89093139  107 RYAMFDVANq-FKIPMFYGIDYEGrhynrylvCYSTVPEHYVDPVIPYLIers-gdRFYIFGYDYi-wPHRMSERIVAEV 183
gi 27375307  124 RNAIKDPIVarGKTLYIYPQLYEGkectpylfCTGPTPAQQCDEFIPWLIkng-gkKFALPSANYv-wPHTLNVYARKVI 201
gi 91781258  131 RNAIKDVIVnrGRTLYIYPQLYEGgentpylfVTGPTPAQQLDPLIPWLIang-gkRFALPGANYv-wPHQLNAYARKVI 208
gi 109645894 350 REIMQHYADq-TKTLYLDTQQTEGgvsshytfCLSAMPEQQMTQMLAYLLqky-grKCYVVAADYn-yGILSAEWVKYLV 426
gi 120612457 114 REAVLQVASr-YRRLVVYPNFDEGrchp-lllTTGLASNQRVVPLIDWAVaqa-gkSFFVLASDIgsnRSTLLPQIEAAI 190
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
1QO0_A       165 rqhgGTVLEEIYIplypsdddLQRAVERIYQAradVVFSTvvgtgTAELYRAIARRygdgrrPPIASLttseae--vakm 242
1QNL_A       165 rqhgGTVLEEIYIplypsdddLQRAVERIYQAradVVFSTvvgtgTAELYRAIARRygdgrrPPIASLttseae--vakm 242
gi 27377955  168 tangGSIVGEKYHpld--hmeYDETVARIMSSgaeVVFNTivppgVVPFFAQLHNAgfqdrgGQLICTyfdenl--lgll 243
gi 13471873  165 rangGEIVGEEYFpld--tvdFRRTVQQIMASrtdVVFNTivppgLTPFLEELHKAgfgkrgGKIVCTyfdenf--fnlv 240
gi 37677088  187 ekveGEISGIEFTafg--vkdYTPVLERIKRSgtnVLMLIlpgsdGFNFLKQMKAFefe-reIQVVAFaadety--lsnv 261
gi 89093139  184 nragGKISGREFTafn--ikdYSAVFERINQAetdNLMLIlpgadGFRFLEQMAEFkfs-kpLKTVAFaadety--lntv 258
gi 27375307  202 esngGEVVFEEYYpld--qvdFSSTVNRIISNkvdVVFNTvippgVGPFFKQLYEAgflkngGRLACVyydent--lnin 277
gi 91781258  209 qehgGEVVLEEYYpld--qvdYGSTVNRIINEkvdVVLATiippgIGPFLKQLHTAgflargGRLSVPyydent--lgis 284
gi 109645894 427 hqlgGEIVGVEYLddr--itdFNPLIDRILQLeadILFSIcvfpnHDAFYLQWHQRgl--nhIPNASTmvaaeayqnvrf 502
gi 120612457 191 qargGRLLGTRFFpfg--trdYGPALQQIQGLgadVVWHSig-ddPVSFVKQYRSFgm---kPQLITDiahes---lams 261
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
1QO0_A       243 eSDVAEGQVVVAPYfssid--tpasRAFVQACHGFfpena--------titaWAEAAYWQTLLLGraaqaaGNWRVEDVQ 312
1QNL_A       243 eSDVAEGQVVVAPYfssid--tpasRAFVQACHGFfpena--------titaWAEAAYWQTLLLGraaqaaGNWRVEDVQ 312
gi 27377955  244 pAPHVEGLYGCLDFyqnvs--dpfsKTLLGAYDKRypgkeq------ftggsACSGLYRGIKLWAaavneaGSLRQKDVI 315
gi 13471873  241 pSDQIEGLYSCLDYyqeld--epfgRALLRRYGERfpggat------ltagsGCTGHYRAIKMWEaavkeaGSAERDAVI 312
gi 37677088  262 dSQSLQGVMTALHFfsgld--navaREFVQNYHRFhgada--------vvtySSKAHYDLIYLIKaaieksGRVDGEQLL 331
gi 89093139  259 kPSALEGVISPLHFvserq--npvfSRFVERYRERygesa--------svtyASKSHYDLIFFFKgalekaGEMDRERML 328
gi 27375307  278 qASEIEGLASCLDYfkvltkenpfdAKIQAAYEKDfpgnfl------faagsAATGTYRGLKLWEaavkeaGKLDRESVA 351
gi 91781258  285 pKEDIEGLATSLDYfhavtatdpvsARIQSEYDKAypnsry-----llaagsAATGTYRAIKLWEaavteaHSVERDPVA 359
gi 109645894 503 aPPVLENMYVMASFieeln--tpaaQRFVKKFRAAydhrev------pymsmDTETVYTAMYVYKravelaGTTDTEEVI 574
gi 120612457 262 tEGALAGTVGVSSYfmgve--npenQRFLDTYTRRfsdatplrvgghvvmlpHGESTYAGAKLFAaaagraGSIEADAVK 339
                        330       340       350
                 ....*....|....*....|....*....|...
Feature 1                                         
1QO0_A       313 RHLYdid--idaPQGPVRVERqNNHSRLSSRIA 343
1QNL_A       313 RHLYdid--idaPQGPVRVERqNNHSRLSSRIA 343
gi 27377955  316 AALDhagi-aegPGGPAEMVPgQHHVRMNMYIA 347
gi 13471873  313 RALDhari-segPGGPAEMVPgQHHVRMNMYIA 344
gi 37677088  332 INLPgl----tlYSGEDAVHLrNDHHFDLPMYL 360
gi 89093139  329 DALEglt--lysGESKVTLRGdNHFNLPMFLAE 359
gi 27375307  352 AALDhaki-aegPGGPAEMVPgKRHCKMKMYTA 383
gi 91781258  360 AALDhaki-aegPGGPAEFVPgQRHVRLRIYTA 391
gi 109645894 575 TALEsgavyvdgPGGRVTVRGeDHHTSRSLSCF 607
gi 120612457 340 KALPgvs--lrmPRGAVGVDAgASHLQCQTMIG 370

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