2NLL


Conserved Protein Domain Family
NR_DBD_TR

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cd06961: NR_DBD_TR 
Click on image for an interactive view with Cn3D
DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers
DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), and being associated with a complex of proteins containing corepressor proteins. Ligand binding promotes corepressor dissociation and binding of a coactivator to activate transcription. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Statistics
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PSSM-Id: 143519
View PSSM: cd06961
Aligned: 15 rows
Threshold Bit Score: 144.481
Threshold Setting Gi: 1942117
Created: 21-Nov-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 8 residues -Click on image for an interactive view with Cn3D
Feature 1:zinc binding site [ion binding site]
Evidence:
  • Structure:2NLL_B; zinc binding site of human Thyroid Hormone Receptor DNA binding domain, contacts determined at 4A
    View structure with Cn3D
  • Comment:Zinc finger, C4-type: The domain contains two groups of four Cys residues. Each group is involved in the co-ordination of a single zinc atom.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1          #  #             #  #                 #      #         #  #                    
2NLL_B          3 LCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLhpSYSCKYEG-KCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSK 81
gi 115732680   76 PCVVCGDAATGYHYRCMTCEGCKGFFRRTIQKKL--SYYCKWNE-ECIIDKTTRNQCQQCRYKKCLNVGMAPDLVLNESQ 152
gi 6093487     34 PCVVCGDDATGLHYRAITCEGCKGFFRRTVQQKI--VYKCKSIE-RCEISKISRNICQFCRFQKCLRNGMTKSLVLNETE 110
gi 70571373    43 ECVVCGDKATGYHYRCITCEGCKGFFRRTVQKDLqkTYQCKQRG-KCQVNKVSRNQCQMCRYEKCIATGMATDLVLNEDK 121
gi 39980016   201 PCVVCGDNATGFHYRAMTCEGCKGFFRRSVQKKL--VYTCKYNGrCSVSDKQNRNSCQKCRFDRCIKGGMAKDLVLDEEK 278
gi 15706340    44 VCVVCGDKATGYHYRCITCEGCKGFFRRTVQKGLhqAYQCKQDE-KCQINKVSRNQCQLCRYKKCITTGMATDLVLNEDK 122
gi 84028527    16 PCVVCGDKATGYHYRCITCEGCKGFFRRTIQKKLhpSYACKFGG-RCAVDRVTRNQCQECRFRKCLAAGMAADLVLDESK 94
gi 151413583   53 PCVVCGDKATGYHYRCMTCEGCKGFFRRTVQKDL--KYSCKYAG-DCVVDKTTRNQCQECRFKKCVRVGMATDLVLDEQK 129
gi 219446909 1668 FCLICNDRASGYHYSVYSCEGCKGFFKRTVQKNL--SYKCKGEG-HCEINKFTRNNCQSCRFQKCMDNGMKKEAVREDRA 1744
gi 16797872    85 ECVVCNDKATGYHYGVFTCEGCKGFFKRTVQKQL--EYTCKGDG-NCEVNQISRNRCQYCRFNKCLAQGMLKEAVREDRT 161

                  ....*...
Feature 1                 
2NLL_B         82 RLAKRKLI 89
gi 115732680  153 RKAKRALI 160
gi 6093487    111 RIAKRKMI 118
gi 70571373   122 RIAKRKLI 129
gi 39980016   279 RLAKRRLI 286
gi 15706340   123 RLAKRRLI 130
gi 84028527    95 RQAKRRLI 102
gi 151413583  130 RVAKRKLI 137
gi 219446909 1745 PGGRQGQK 1752
gi 16797872   162 PGGRHRHR 169

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