1FM6,2J14


Conserved Protein Domain Family
NR_LBD_PPAR

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cd06932: NR_LBD_PPAR 
Click on image for an interactive view with Cn3D
The ligand binding domain of peroxisome proliferator-activated receptors
The ligand binding domain (LBD) of peroxisome proliferator-activated receptors (PPAR): Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response element located upstream of the peroxisome proliferator responsive genes and interacts with co-activators. There are three subtypes of peroxisome proliferator activated receptors, alpha, beta (or delta), and gamma, each with a distinct tissue distribution. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR has a central well conserved DNA binding domain (DBD), a variable N-terminal regulatory domain, a flexible hinge a nd a C-terminal ligand binding domain (LBD).
Statistics
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PSSM-Id: 132730
View PSSM: cd06932
Aligned: 9 rows
Threshold Bit Score: 302.023
Threshold Setting Gi: 72164991
Created: 19-Nov-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 10 residues -Click on image for an interactive view with Cn3D
Feature 1:ligand binding site [chemical binding site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
1FM6_D         4 ADLRALAKHLYDSYIKsfpltkaKARAILTGKttdkspfviydmnslmmge----------------------------- 54
2J14_A        17 ADLKAFSKHIYNAYLKnfnmtkkKARSILTGKashtapfvihdietlwqae----------------------------- 67
gi 47825369  207 ADLRALAKHLYDSYIKsfpltkaKARAILTGKttdkspfviydmnslrmge----------------------------- 257
gi 82240332  230 ADLRALARHLYEAYLKyfpltkaKARAILSGKtgdnapfvihdikslmegeqfincrqmpiqeqqqas------------ 297
gi 122049643 176 TKLVSPCDEMLTPDLKarllfasQVFKKNIGKdkptiykn---------------------------------------- 215
gi 585720    129 SDLDVLSQLIHSSYMNtftmtkkRARDILTGRnsispfvihdmdtlwqaeq----------------------------- 179
gi 72164991  137 RIHSIYINMWMGQFISmpvgsraTRSKEPNGKtedhksm----------------------------------------- 175
gi 115899356 219 VDSIAQQFNDIVCAMTqed--leKFWKRCSRPftahmpsgtyviegm--------------------------------- 263
gi 16565492   95 SDLRSLARLVQEAYLRifplskaKAQAILAGKvqnnavvihdheslaqaedtilqksgygtihnhgsigvniasvgggcg 174
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                            ##   #      
1FM6_D        55 --------------------------------------------dkikfkhitplqeqskevaIRIFQGCQFRSVEAVQE 90
2J14_A        68 --------------------------------------------kglvwkqlvnglppykeisVHVFYRCQCTTVETVRE 103
gi 47825369  258 --------------------------------------------dqikckhasplqeqnkevaIRIFQRCQFRSVEAVQE 293
gi 82240332  298 ---------------------------vltathggltehhmgsdygvwgttsisgqepqnaleLRFFQSCQSRSAEAVRE 350
gi 122049643 216 --------------------------------------------------------vigskivQILYSDFQARVVNGICE 239
gi 585720    180 ---------------------------------------------gtvweqlptqnltgteigVHVFYRCQCTSVETVRA 214
gi 72164991  176 ---------------------------------------------------------keltekEALTKFCRGALLAIIES 198
gi 115899356 264 -------------------------------------------------qlnkdgppqeitsrAEMAQQCFVSMEVTIEK 294
gi 16565492  175 garggticdgrggpcdsttrgrvlgtdcvfitansvtdtelaadaegnrssdqevtpprgaaeIRIFNRCHYRLVEAVRE 254
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                   #   #  #        # #                      #           
1FM6_D        91 ITEYAKSIPGFvnLDLNDQVTLLKYGVHEIIYTMLASLMNKdGVLISEGQGFMTREFLKSLRkpfgDFMEPKFEFAVKFN 170
2J14_A       104 LTEFAKSIPSFssLFLNDQVTLLKYGVHEAIFAMLASIVNKdGLLVANGSGFVTREFLRSLRkpfsDIIEPKFEFAVKFN 183
gi 47825369  294 ITEFAKNIPGFvnLDLNDQVTLLKYGVHEIIYTLLASLMNKdGVLISDGQGFMTREFLKSLRkpfcDFMEPKFEFAVKFN 373
gi 82240332  351 VTEFAKSIPGFtdLDLNDQVTLLKYGVIEVLIIMMSPLMNKdGTLISYGQIFMTREFLKSLRkpfcQMMEPKFEFSVKFN 430
gi 122049643 240 LTEFAKRLPNFhdISLQDQVILLKYGSYETMFVLFSRLIYGeGMILPKSNIYVTFNFVYQLGva-gDIMKSKFLFAKKML 318
gi 585720    215 LTDFAKRIPGFgtLYLNDQVTLLKYGVHEAIFCMLASLMNKdGLLVAGGRGFVTREFLRSLRqpfcHIMEPKFHFASKFN 294
gi 72164991  199 LAKFAKKLQEFknLDLNDQVCLLKHAAFEVALIATSSRYASeGLWFPTDGVYFTKKMLEQLEi---SFFDGKFKFFEKMK 275
gi 115899356 295 FATFAKQLPEFrrLSSSDQLTLFKGAALEVCATLSASRYYHgVYRFPEINTYIRRDVAENSPfgkvTTYTTEMMFYEMFN 374
gi 16565492  255 VTEFAKSIPGFmiLDLNDQVTLLKYGVYEVIFAMLAAQINKdGLLIAYGSAFITREFLRSLRspfcHIMEPKFEFSIRFN 334
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                 #      
1FM6_D       171 aLELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPessQLFAKLLQKMTDLRQIVTEHVQLLQV 250
2J14_A       184 aLELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPdaqYLFPKLLQKMADLRQLVTEHAQMMQR 263
gi 47825369  374 aLELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPessQLFAKLLQKMTDLRQIVTEHVQLLQI 453
gi 82240332  431 tLELDDSDMALFLVVIILSGDRPGLLNVKPIEQLQETVLHSLELQLKLNHPdslQLFAKLLQKMTDLRQIVTDHVHLIQL 510
gi 122049643 319 aLELTDDEMALFVAMIILCPDRPEINDRKLVERIQEKVLFALEYQLSISHPhkpRLFAHLLLKMAELRELVSKHVVMVQK 398
gi 585720    295 aLELNDSDLALFVASIILCGDRPGLINPSQVEDIQEGILGALRRHLKASHTdapFLFPKLLHKMADLRQLVTEHAELVQS 374
gi 72164991  276 kLNLTERELALFCVLSLTSPDRDELIERDEVEKFQEQVLEAIQIELRTNHSnhrMLLPRLLSLLVDLRQLVLDHIKQVQQ 355
gi 115899356 375 eLGLTDKEKAVFCTFLLYSPDREGLVDREVVERHQEHLAQILYLEVKKNHPdrsNLYAKLMDVAVALRTLVPDHLARLEQ 454
gi 16565492  335 aLSLDGTDLALYMAAIILCGDRPGLINVNPVERIQDRILQALDLQLRKTHPespFLFPKLLQKLSDLRQLVTEHAQMVHN 414
                        330       340
                 ....*....|....*....|....
Feature 1                                
1FM6_D       251 IKKtet---dmsLHPLLQEIYKDL 271
2J14_A       264 IKKtet---etsLHPLLQEIYKDM 284
gi 47825369  454 IKKtet---dmsLHPLLQEIYKDL 474
gi 82240332  511 LKKtev---dmcLHPLLQEIMKDL 531
gi 122049643 399 LADak-----dfVPPLLCEIMQDM 417
gi 585720    375 IKRtes---saaLHPLLQEIYRDM 395
gi 72164991  356 LMLmddp-sysgPPPLIKEIFGLY 378
gi 115899356 455 IKMrcnghlpaePSPLLNEVYGSI 478
gi 16565492  415 IRKtea---dtaLPPLLQEIFKDM 435

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