1QNL,1PEA,1QO0


Conserved Protein Domain Family
PBP1_AmiC

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cd06357: PBP1_AmiC 
Click on image for an interactive view with Cn3D
Periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family
This group includes the periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family. AmiC controls expression of the amidase operon by the 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 are induced.
Statistics
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PSSM-Id: 107352
View PSSM: cd06357
Aligned: 25 rows
Threshold Bit Score: 448.612
Threshold Setting Gi: 114764664
Created: 23-Jul-2007
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
ligand bindingregulator
Conserved site includes 9 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                                                                                  ###   
1QNL_A         9 LIGLLFSETGvtadIERSQRYGALLAVEQLNReggvgGRPIETLSQDPggdpDRYRLCAEDFIRnRGVRFLVGCYMSHTR 88
1PEA_A         9 LIGLLFSETGvtadIERSQRYGALLAVEQLNReggvgGRPIETLSQDPggdpDRYRLCAEDFIRnRGVRFLVGCYMSHTR 88
1QO0_A         9 LIGLLFSETGvtadIERSQRYGALLAVEQLNReggvgGRPIETLSQDPggdpDRYRLCAEDFIRnRGVRFLVGCYMSHTR 88
gi 15965708    8 PVGVLFSRSGsyaqPAGQGFGGAMAAIEHVNAsr-rfPFRLEAHHFDPageaDRYAPFCRQLIReHGVRHVVGCTTSWSR 86
gi 91978754    7 PVGILTSKSGpyqaMGREILKCALMAIDDVNDcp-dfGFRFTPHVRDPggviSAYHTACDDLIRnVRVEHIIGCYTSASR 85
gi 92112343   27 AVGLLYSTTGtyqrISNNARSGALQAVADINAda-tsGVTLVAHEYDPhgelEAYHRGVEDLLA-RGVRHVVGTTTSASR 104
gi 114764664   6 DLGILFSRSGtyslISEAKRTGALKAVAQVNAdp-alDIVFNPVERDPqgniDAYAPLCEEILRdSGARHVIGCTTSWSR 84
gi 116255653   6 KIGILFSTTGpygsMGRDARDGADFAMAEYAGv---eGVAIEPIFFDPhadlAAYLDGARHLLR-AGCRHIVGTITSAAR 81
gi 118592900   7 PVGVLFSKSGsyaaIGQEGYWGARIAIDEINAsg-lfDFRFLRVDGDPkgsaENYAVEAERMMReAGCRHIIGTQTSSSR 85
gi 160899073   6 RVGILYSATGttstIGQSQLQGAQLAIDEINEtggllGRELVAVRYDPastpARYAALAEQLIVrDGINVIFGCYMSSSR 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                       #  ##                                         # #                
1QNL_A        89 KAVMPVVErADALLCYPNPYEGFEYspNIVYGGPAPNQNSAPLAAYLIrhygeRVVFIGSDYIYPRESNHVMRHLYrq-h 167
1PEA_A        89 KAVMPVVErADALLCYPTPYEGFEYspNIVYGGPAPNQNSAPLAAYLIrhygeRVVFIGSDYIYPRESNHVMRHLYrq-h 167
1QO0_A        89 KAVMPVVErADALLCYPTPYEGFEYspNIVYGGPAPNQNSAPLAAYLIrhygeRVVFIGSDYIYPRESNHVMRHLYrq-h 167
gi 15965708   87 KEVIPVVEkLDALLWYPCVYEGFEVseNLIYVAACANQHLVPLLDYIAprfgsRAMLVGSNYIWGWETNRIARDILhr-s 165
gi 91978754   86 KQVLPIVErTERLLWYPARYEGFECsdNVIYVGASPNHNVVPLIRYVLdnlsrDFFCVGSNYVWTWETNRVTRELVta-a 164
gi 92112343  105 KDIVPDVErDEALLWYACPYEGFECseNVLYSGGCPSQNLVPLLAYALrergkRGVLIGSNYVWGWESNRIARELVea-s 183
gi 114764664  85 KEVIPALErMDGALWYPAPYEGFEAsdRIVYAHACPNQHLLPLLDYAFaqfgrRSYLTGSNYIWGWEINRLAREIGsr-t 163
gi 116255653  82 KEVIPLVEkHDGLLWYMCPYEGFEAneNVIYVGGCPNQHLLPLFEHLIprygaRPYLVGANYVWGWEMNRLARELItn-a 160
gi 118592900  86 KEVLPVMErGRGLLWYTTPYEGFEShdRVVYTGACPNQGVVPLFRHIVpesgrRAFLLGSNYIWGWETNRIARELLag-c 164
gi 160899073  86 KAVIPIVEkWNKLLFYPTLYEGFEFsgNVIYTGAAPNQNSVQLADYMTssfgaRVYLIGSDYIYPYESNRIMGELVmqhp 165
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                              #         
1QNL_A       168 gGTVLEEIYIplypsdddLQRAVERIYQAradVVFSTvvgtgTAELYRAIARRygd-----grrPPIASLTTseaevakm 242
1PEA_A       168 gGTVLEEIYIplypsdddLQRAVERIYQAradVVFSTvvgtgTAELYRAIARRygd-----grrPPIASLTTseaevakm 242
1QO0_A       168 gGTVLEEIYIplypsdddLQRAVERIYQAradVVFSTvvgtgTAELYRAIARRygd-----grrPPIASLTTseaevakm 242
gi 15965708  166 gGEILGERFVsmg--dtdIAHLIDEVREKkpdFILNNligpsSYAFLRALQALaeaddrfhpdrCPVISCNLyege-iag 242
gi 91978754  165 eGHIVAERLLelg--esrVDHIVEEIVRRqppIVFNTlvgssSYDFIRAFQSAtaaa----glnIPMLSCSLcepe-lri 237
gi 92112343  184 hGRIVAEKYFhfg--dcdFEAIVPRILEGaadFVLNNlvgesSYAFLAQLEAAcerq----gtgITVLSCNFtecelpai 257
gi 114764664 164 gGEVLGERYLplg--tteVARIVDEIAALkpdFVLNQligksQYAFLDAIAELrrsdpffaeghCPVLSCNLtece-lga 240
gi 116255653 161 gGEVLGERYLple--etaVERIVAEIAQRrpsFILNNligpsSYAFLEAIKALgdrdpafhaenCPVVSCDLmecelddi 238
gi 118592900 165 dGEVLGERYVaig--denIDHLIVEIREKrpdFIFNNligesSYAFLRAMKRLakedpafapnrCPILSCNLteae-lpv 241
gi 160899073 166 gSDKLGEHYLpldaterdYAAIMQDIRARqpdFIFSTvvgdsTASLYRAYADAgfn-----pqtMPIASLTTseaeiaqm 240
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
1QNL_A       243 eSDVAEGQVVVAPYFssidtpasRAFVQACHGFFpenatitaWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYdidida 322
1PEA_A       243 eSDVAEGQVVVAPYFssidtpasRAFVQACHGFFpenatitaWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYdidida 322
1QO0_A       243 eSDVAEGQVVVAPYFssidtpasRAFVQACHGFFpenatitaWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYdidida 322
gi 15965708  243 lGHAAAGHFTVSCYFrtiqspenDSFLKTLAALDpgav-vdaFYVQAFSAVVMIAEAIARSGSDDADLVRAALCgqavdt 321
gi 91978754  238 vGPAAAGCITSSAYFesirlpenRAFVARWKARYgkdsspsvDGQSAYVATFLLARAMQRAGTSNVNEVRRAAAgyryds 317
gi 92112343  258 pRLRHVRLLSCGPWFdh----pgNGFSARQRVRHgaqi-yssCYTNAYNAVQLLARGCDAVGSDDPSKVLAWLHatshst 332
gi 114764664 241 iGPSAEGVISAGPWFrgl---hpALPGNGGREDFg------sSLEAAAHASVMTLAQLLNGAPGAEALSLSELLaq---r 308
gi 116255653 239 aAGAAAGQLCAASYFdsiatpenAAFKARVTERHgaerrvssVFASAYTAVRLCVDAIVAAGSDEPDAVRRELYnrswpt 318
gi 118592900 242 lGAAAEGLVSTSTYFetldtpenQDFLSRLEGLRgpdasissMFVGPYEAVWLLARAIEACGSDAPDHVLAELCrrphrt 321
gi 160899073 241 gADVAAGHFTAAPYFqsidspanARCLARLRQRLgddcrpnlCWEAAYFQMHLFANAFRQAGSDRIGELLPHLLgsefda 320
                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|..
Feature 1                                                            
1QNL_A       323 PQGPVRVERQNNHSRLSSRIAeidarGVFQVRWqs------pePIRPDPYVV 368
1PEA_A       323 PQGPVRVERQNNHSRLSSRIAeidarGVFQVRWqs------pePIRPDPYVV 368
1QO0_A       323 PQGPVRVERQNNHSRLSSRIAeidarGVFQVRWqs------pePIRPDPYVV 368
gi 15965708  322 PLGAISVDRWTNHVELPAHIGragadGSFEIVKrs------yeAIAPDPFLT 367
gi 91978754  318 PQGPVWIDGDNNHCVLTPRLAvsnarGQFDIFWea------eaPVKPDPYLS 363
gi 92112343  333 LMGELAFNPRNNHLALPCCIAeagdeGFRIVHRes-------gVRDADPYLT 377
gi 114764664 309 RAAELGISPRTHHTRLPVAIAqv-raGAFVPLRtg-------aPVEADPYLT 352
gi 116255653 319 LFGALSIDRDTNHAALPFHLGrinadNGFDVVAsr-------pPLAADPYLT 363
gi 118592900 322 PLRDIRIDPQTQHAYLQPLIAvvettGPERPRSrfriiektsgPLAPDPYLV 373
gi 160899073 321 PQGRIRLDPDNHHTWLHPRVGranaqGGFTIVRqa------trAVSPDPYLV 366

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