1KB6,1YNW,1KB2


Conserved Protein Domain Family
NR_DBD_VDR_like

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cd07156: NR_DBD_VDR_like 
Click on image for an interactive view with Cn3D
The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers
The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family 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. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. Like other nuclear receptors, xenobiotic receptors have 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: 143531
View PSSM: cd07156
Aligned: 17 rows
Threshold Bit Score: 121.72
Threshold Setting Gi: 61680752
Created: 3-Feb-2009
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, 3.5 A contacts
    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         9 CGVCGDRATGFHFNAMTCEGCKGFFRRSMKRkALFTCPFNgdCRITKDNRRHCQACRLKRCVDIGMMKEFIL 80  human
NP_001041239  84 CRVCGDHATGYNFNVITCESCKAFFRRNALRpKEFKCPYSedCEINSVSRRFCQKCRLRKCFTVGMKKEWIL 155 nematode
NP_001079364  37 CRACGDRATGYHFNAMTCEGCKGFFRRAMKRnLRLSCPFQnsCVINKSNRRHCQACRLKKCLDIGMRKELIM 108 African clawed frog
NP_001071847 157 CGVCNDKATGYHFNALTCEGCKGFFRRSVKNsKTFTCTYNnqCSITKSNRRQCQACRLRKCIQIGMKRECIM 228 Ciona intestinalis
XP_001371998  11 CVVCGDRATGYHFHALTCEGCKGFFRRTINKgMGLTCPFDqcCEVSKNQRRHCPACRLQKCLDVGMKKDMIL 82  gray short-tailed opossum
EEC00893      90 CGVCGDRAKSYHFGGISCDSCKAFFRRSVQNeARFTCPYQgrCHITLTSRKSCQACRFAKCLSIGMEASWVM 161 black-legged tick
NP_990033     31 CAVCGDRATGYHFHVMSCEGCKGFFRRSILKgVHFTCPFTrsCPITKAKRRQCQACRLQKCLDVGMRKDMIM 102 chicken
Q8MIM3        11 CVVCGDQATGYHFNALTCEGCKGFFRRTVSKsIGPTCPFAgsCEVSKIQRRHCPACRLQKCLDAGMRKDMIL 82  rhesus monkey
CAG05861       5 CGVCGDQARGYHFNAWTCEGCKGFFRRAIKRtVQLYCPFLnkCSITKKNRRQCQACRLRKCQAIGMRQEMVM 76  spotted green pufferfish
ABR21208      38 CGVCGDLAKGYHFNALTCEGCKGFFRRAIKRsTQLRCPFLnkCIITKNNRRSCQACRFRKCQAIGMRKDMVM 109 killifish

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