1XAP,1XDK,1DKF


Conserved Protein Domain Family
NR_LBD_RAR

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cd06937: NR_LBD_RAR 
Click on image for an interactive view with Cn3D
The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to an inactive condensed chromatin structure, preventing transcription. Upon ligand binding, the corepressors are released, and coactivator complexes such as histone acetyltransferase or histone arginine methyltransferases are recruited to activate transcription. There are three RAR subtypes (alpha, beta, gamma), originating from three distinct genes. For each subtype, several isoforms exist that differ in their N-terminal region, allowing retinoids to exert their pleiotropic effects. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoic acid receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Statistics
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PSSM-Id: 132735
View PSSM: cd06937
Aligned: 9 rows
Threshold Bit Score: 401.498
Threshold Setting Gi: 115681476
Created: 19-Nov-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 16 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                                                     #  ##  #                           
1XAP_A        32 DLTEKIRKAHQETFPslcqLGKYTTNSsadh---rvrLDLGLWDKFSELATKCIIKIVEFAKRLPGFTgLTIADQITLLK 108
gi 122049638 400 ALVTSVHKFHVETFPlsseLKKYQIPSppivkdtsakTDSNLWEKFAELSTKCIVKIVEFAKGIPGFQdFTIADQITLLK 479
gi 3041719   186 DLTEKIRKAHQETFPslcqLGKYTTNSsadh---rvrLDLGLWDKFSELATKCIIKIVEFAKRLPGFTsLTIADQITLLK 262
gi 28558767  209 ELIQKVSKAHQETFPslcqLGKYTTNSsadq---rvqLDLGLWDKFSELSTKCIIKIVEFAKRLPGFTtLTIADQITLLK 285
gi 118572702 176 ELVNKVSKAHQETFPslcqLGKYTTNSssdh---riqLDLGLWDKFSELSTKCIIKIVEFAKRLPGFTtLTIADQITLLK 252
gi 115681476 134 DILQEVLRAHRDTFPqrplHPIHNAVSagn-----idIDMVMFDYVTDMSSRAIVMVVDFAKKLPGFLsLSTQDQITLLK 208
gi 219413150 179 TIITTVREAHMATLPdmgkLPKYKVKNaaeq---rgpTDIELWQHFSDLCTETIIKIVQFAKKVPGFTtFGTADQITLLK 255
1XDK_B        34 DLTEKIRKAHQETFPslcqLGKYTTNSsadh---rvrLDLGLWDKFSELATKCIIKIVEFAKRLPGFTgLTIADQITLLK 110
1DKF_B         5 ELIEKVRKAHQETFPalcqLGKYTTNNsseq---rvsLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTtLTIADQITLLK 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1           #  ##  #  #         ##              #                                        
1XAP_A       109 AACLDILILRICTRYTPEQDTMTFSdGLTLNRTQMHNAGFGPLTDLVFTFANQLlpLEMDDTETGLLSAICLICGDRqdL 188
gi 122049638 480 CACLEVLFLRICSRFSPEHDTMTFSdGLTLTRKQMRVCGFGPITEQVFSFAQSLhpLNADATEIGLLSAICLVSADRvdL 559
gi 3041719   263 AACLDILILRICTRYTPEQDTMTFSdGLTLNRTQMHNAGFGPLTDLVFTFANQLlpLEMDDTETGLLSAICLICGDRqdL 342
gi 28558767  286 SACLDILMLRICTRYTPEQDTMTFSdGLTLNRTQMHNAGFGPLTDLVFSFADQLlpLEMDDTETGLLSAICLICGDRmdL 365
gi 118572702 253 SACLDILMLRICTRYTPEQDTMTFSdGLTLNRTQMHNAGFGPLTDLVFAFAGQLlpLEMDDTETGLLSAICLICGDRmdL 332
gi 115681476 209 ASCLDIMILRICSRFNPQDASVTFTtGLTLTQGQLKAGGFGSLLDVIFTFASSLsrMHIDETEIALLSAICLISEDRtgL 288
gi 219413150 256 AACLDILILRLATRLDKESDTVTFInGMMLSRTQMHNAGFGPLTDGVFTFAEGMqkLLFDETEIGLMCSICLVCGDRqgL 335
1XDK_B       111 AACLDILILRICTRYTPEQDTMTFSdGLTLNRTQMHNAGFGPLTDLVFTFANQLlpLEMDDTETGLLSAICLICGDRqdL 190
1DKF_B        82 AACLDILILRICTRYTPEQDTMTFSdGLTLNRTQMHNAGFGPLTDLVFAFANQLlpLEMDDAETGLLSAICLICGDRqdL 161
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
Feature 1                                                           ##  #                #  
1XAP_A       189 EEPTKVDKLQEPLLEALKIYIRKRRPskphMFPKILMKITDLRSISAKGAERVITL-KMEIPGSMPPLIQEMLEN 262
gi 122049638 560 EEPDKVELLQESLVEGLKYYARKRRPhtpqVFPKLIIKISDLRSISLKGADRVVTVkTEIPCGAMPPLMSEMLEN 634
gi 3041719   343 EEPMKVDKLQEPLLEALKIYIRKRRPnkphMFPKILMKITDLRSISAKGAERVITL-KMEIPGSMPPLIQEMLEN 416
gi 28558767  366 EEPEKVEKLQEPLLEALKFYARRRRPdkpyMFPRMLMKITDLRGISTKGAERAITL-KLEIPGPMPPLIREMLEN 439
gi 118572702 333 EEPERVDRLQEPLLEALKIYARRRRPnkphMFPRMLMKITDLRGISTKGAERAITL-KMEIPGPMPPLIREMLEN 406
gi 115681476 289 EDAPRIEKMQEPLLEGLRLYVRKRRPkeshFFAKLLMKITDLRCISVKSAEKVFDM-KVEFVKEMPALISEMIDK 362
gi 219413150 336 EDIQRAENLQEPLLEALKAYSRRRIPddpqRFPKMIMKITDLRSISSKGAERVITL-KMELSSPMPPLIAEIWEK 409
1XDK_B       191 EEPTKVDKLQEPLLEALKIYIRKRRPskphMFPKILMKITDLRSISAKGAERVITL-KMEIPGSMPPLIQEMLEN 264
1DKF_B       162 EQPDRVDMLQEPLLEALKVYVRKRRPsrphMFPKMLMKITDLRSISAKGAERVITL-KMEIPGSMPPLIQEMLEN 235

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