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:
Feature 1                                                     #  ##  #                           
1XAP_A        32 DLTEKIRKAHQETFPslcqLGKYTTNSsadh---rvrLDLGLWDKFSELATKCIIKIVEFAKRLPGFTgLTIADQITLLK 108 human
Q4H2W2       400 ALVTSVHKFHVETFPlsseLKKYQIPSppivkdtsakTDSNLWEKFAELSTKCIVKIVEFAKGIPGFQdFTIADQITLLK 479 Ciona intestinalis
P22448       186 DLTEKIRKAHQETFPslcqLGKYTTNSsadh---rvrLDLGLWDKFSELATKCIIKIVEFAKRLPGFTsLTIADQITLLK 262 chicken
P28699       209 ELIQKVSKAHQETFPslcqLGKYTTNSsadq---rvqLDLGLWDKFSELSTKCIIKIVEFAKRLPGFTtLTIADQITLLK 285 African clawed ...
Q91392       176 ELVNKVSKAHQETFPslcqLGKYTTNSssdh---riqLDLGLWDKFSELSTKCIIKIVEFAKRLPGFTtLTIADQITLLK 252 zebrafish
XP_779976    134 DILQEVLRAHRDTFPqrplHPIHNAVSagn-----idIDMVMFDYVTDMSSRAIVMVVDFAKKLPGFLsLSTQDQITLLK 208 purple urchin
XP_002204386 179 TIITTVREAHMATLPdmgkLPKYKVKNaaeq---rgpTDIELWQHFSDLCTETIIKIVQFAKKVPGFTtFGTADQITLLK 255 Florida lancelet
1XDK_B        34 DLTEKIRKAHQETFPslcqLGKYTTNSsadh---rvrLDLGLWDKFSELATKCIIKIVEFAKRLPGFTgLTIADQITLLK 110 house mouse
1DKF_B         5 ELIEKVRKAHQETFPalcqLGKYTTNNsseq---rvsLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTtLTIADQITLLK 81  human
Feature 1           #  ##  #  #         ##              #                                        
1XAP_A       109 AACLDILILRICTRYTPEQDTMTFSdGLTLNRTQMHNAGFGPLTDLVFTFANQLlpLEMDDTETGLLSAICLICGDRqdL 188 human
Q4H2W2       480 CACLEVLFLRICSRFSPEHDTMTFSdGLTLTRKQMRVCGFGPITEQVFSFAQSLhpLNADATEIGLLSAICLVSADRvdL 559 Ciona intestinalis
P22448       263 AACLDILILRICTRYTPEQDTMTFSdGLTLNRTQMHNAGFGPLTDLVFTFANQLlpLEMDDTETGLLSAICLICGDRqdL 342 chicken
P28699       286 SACLDILMLRICTRYTPEQDTMTFSdGLTLNRTQMHNAGFGPLTDLVFSFADQLlpLEMDDTETGLLSAICLICGDRmdL 365 African clawed ...
Q91392       253 SACLDILMLRICTRYTPEQDTMTFSdGLTLNRTQMHNAGFGPLTDLVFAFAGQLlpLEMDDTETGLLSAICLICGDRmdL 332 zebrafish
XP_779976    209 ASCLDIMILRICSRFNPQDASVTFTtGLTLTQGQLKAGGFGSLLDVIFTFASSLsrMHIDETEIALLSAICLISEDRtgL 288 purple urchin
XP_002204386 256 AACLDILILRLATRLDKESDTVTFInGMMLSRTQMHNAGFGPLTDGVFTFAEGMqkLLFDETEIGLMCSICLVCGDRqgL 335 Florida lancelet
1XDK_B       111 AACLDILILRICTRYTPEQDTMTFSdGLTLNRTQMHNAGFGPLTDLVFTFANQLlpLEMDDTETGLLSAICLICGDRqdL 190 house mouse
1DKF_B        82 AACLDILILRICTRYTPEQDTMTFSdGLTLNRTQMHNAGFGPLTDLVFAFANQLlpLEMDDAETGLLSAICLICGDRqdL 161 human
Feature 1                                                           ##  #                #  
1XAP_A       189 EEPTKVDKLQEPLLEALKIYIRKRRPskphMFPKILMKITDLRSISAKGAERVITL-KMEIPGSMPPLIQEMLEN 262 human
Q4H2W2       560 EEPDKVELLQESLVEGLKYYARKRRPhtpqVFPKLIIKISDLRSISLKGADRVVTVkTEIPCGAMPPLMSEMLEN 634 Ciona intestinalis
P22448       343 EEPMKVDKLQEPLLEALKIYIRKRRPnkphMFPKILMKITDLRSISAKGAERVITL-KMEIPGSMPPLIQEMLEN 416 chicken
P28699       366 EEPEKVEKLQEPLLEALKFYARRRRPdkpyMFPRMLMKITDLRGISTKGAERAITL-KLEIPGPMPPLIREMLEN 439 African clawed frog
Q91392       333 EEPERVDRLQEPLLEALKIYARRRRPnkphMFPRMLMKITDLRGISTKGAERAITL-KMEIPGPMPPLIREMLEN 406 zebrafish
XP_779976    289 EDAPRIEKMQEPLLEGLRLYVRKRRPkeshFFAKLLMKITDLRCISVKSAEKVFDM-KVEFVKEMPALISEMIDK 362 purple urchin
XP_002204386 336 EDIQRAENLQEPLLEALKAYSRRRIPddpqRFPKMIMKITDLRSISSKGAERVITL-KMELSSPMPPLIAEIWEK 409 Florida lancelet
1XDK_B       191 EEPTKVDKLQEPLLEALKIYIRKRRPskphMFPKILMKITDLRSISAKGAERVITL-KMEIPGSMPPLIQEMLEN 264 house mouse
1DKF_B       162 EQPDRVDMLQEPLLEALKVYVRKRRPsrphMFPKMLMKITDLRSISAKGAERVITL-KMEIPGSMPPLIQEMLEN 235 human

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