2E6R


Conserved Protein Domain Family
PHD1_KDM5C_5D

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cd15604: PHD1_KDM5C_5D 
Click on image for an interactive view with Cn3D
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
The family includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C (also termed Histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, SmcX, or Xe169) is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D (also termed Histocompatibility Y antigen (H-Y), Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or SmcY) is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 andH3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.
Statistics
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PSSM-Id: 277077
Aligned: 4 rows
Threshold Bit Score: 53.692
Created: 12-Aug-2013
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Zn binding siteputative
Conserved site includes 8 residues -Click on image for an interactive view with Cn3D
Feature 1: Zn binding site [ion binding site], 8 residue positions
Conserved feature residue pattern:C C C C H C C CClick to see conserved feature residue pattern help
Evidence:
  • Structure:2E6R; Human KDM5D binds two Zn2+ ions through its first PHD finger.
  • Comment:The PHD zinc finger is characterized as Cys4HisCys3.
  • Citation:PMID 7583761
  • Citation:PMID 7701562

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1          #  #           #  #    #  #              #  #
2E6R_A         18 ICQVCSRGDEDDKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKC 63   human
NP_001116706  360 VCRMCGRGDEDEKLMLCDGCDDNYHTFCLIPPLTDPPKGNWRCPKC 405  zebrafish
NP_001072719  350 ICRICSRGDDDDRLLLCDGCDDNYHTFCLLPPLPEPPKGIWHCPKC 395  western clawed frog
NP_001269551  325 VCRMCSRGDEDDKLLLCDGCDDNYHIFCLLPPLPEIPKGVWRCPKC 370  human

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