1KB6,1YNW,1KB2


Conserved Protein Domain Family
NR_DBD_VDR

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cd06955: NR_DBD_VDR 
Click on image for an interactive view with Cn3D
DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers
DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms a heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and even more genes are regulated indirectly. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, VDR 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: 143513
View PSSM: cd06955
Aligned: 7 rows
Threshold Bit Score: 184.377
Threshold Setting Gi: 61680752
Created: 24-Nov-2008
Updated: 2-Oct-2020
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:1KB6_B, Zn binding site of human Vdr Dna-Binding Domain, contacts at 3.5A
    View structure with Cn3D
  • Comment:Zinc finger, C4-type: The domain contains two groups of four Cys residues. Each group is involved in the coordination of a single zinc atom.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1             #  #             #  #               #     #         #  #                
1KB6_B      1 FDRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGdCRITKDNRRHCQACRLKRCVDIGMMKEFIL 80  human
Q1L673     15 FDRNVPRICGVCGDKATGFHFNAMTCEGCKGFFRRSMKRKASFTCPFNGsCTITKDNRRHCQACRLKRCLDIGMMKEFIL 94  zebrafish
O13124     17 FDKNVPRICGVCGDKATGFHFNAMTCEGCKGFFRRSMKRKAMFTCPFNGdCRITKDNRRHCQSCRLKRCVDIGMMKEFIL 96  African clawed frog
O42392     39 FDRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKAMFTCPFNGdCKITKDNRRHCQACRLKRCVDIGMMKEFIL 118 chicken
AAP05810   19 EEGGVPKVCGVCGDKATGYHFNAMTCEGCKGFFRRSMKRSASFTCPFEGkCNITKDNRRHCQACRLKRCRDIGMMKELIM 98  sea lamprey
1YNW_A      1 FDRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCAANGdCRITKDNRRACQACRLKRCVDIGMMKEFIL 80  human
1KB2_A      1 FDRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGdCRITKDNRRHCQACRLKRCVDIGMMKEFIL 80  human
Feature 1                                
1KB6_B     81 TDEEVQRKREMILKRKEEEALKDSLRP 107 human
Q1L673     95 TDEEVQRKKELIQRRKDEEAHREAQKP 121 zebrafish
O13124     97 TDEEVQRKRQMINKRKSEEALKESMRP 123 African clawed frog
O42392    119 TDEEVQRKREMILKRKEEEALKESLKP 145 chicken
AAP05810   99 TEEEVQRKKEIIMKRKLEDSAREVHTP 125 sea lamprey
1YNW_A     81 TDEEVQRKREMILKRKEEEALKDSLRP 107 human
1KB2_A     81 TDEEVQRKREMILKRKEEEALKDSLRP 107 human

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