PHD finger
| PHD-finger | |||||||||
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PHD zinc finger. Zinc atoms shown in grey
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| Identifiers | |||||||||
| Symbol | PHD | ||||||||
| Pfam | PF00628 | ||||||||
| Pfam clan | CL0390 | ||||||||
| InterPro | IPR019787 | ||||||||
| PROSITE | PS50016 | ||||||||
| SCOP | 1f62 | ||||||||
| SUPERFAMILY | 1f62 | ||||||||
| OPM superfamily | 62 | ||||||||
| OPM protein | 1vfy | ||||||||
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| Available protein structures: | |
|---|---|
| Pfam | structures |
| PDB | RCSB PDB; PDBe; PDBj |
| PDBsum | structure summary |
The PHD finger was discovered in 1993 as a Cys4-His-Cys3 motif in the plant homeodomain (hence PHD) proteins HAT3.1 in Arabidopsis thaliana and maize ZmHox1a. The PHD finger motif resembles the metal binding RING domain (Cys3-His-Cys4) and FYVE domain. It occurs as a single finger, but often in clusters of two or three, and it also occurs together with other domains, such as the chromodomain and the bromodomain.
The PHD finger, approximately 50-80 amino acids in length, is found in more than 100 human proteins. Several of the proteins it occurs in are found in the nucleus, and are involved in chromatin-mediated gene regulation. The PHD finger occurs in proteins such as the transcriptional co-activators p300 and CBP, Polycomb-like protein (Pcl), Trithorax-group proteins like ASH1L, ASH2L and MLL, the autoimmune regulator (AIRE), Mi-2 complex (part of histone deacetylase complex), the co-repressor TIF1, the JARID1-family of demethylases and many more.
The NMR structure of the PHD finger from human WSTF (Williams Syndrome Transcription Factor) shows that the conserved cysteines and histidine coordinate two Zn2+ ions. In general, the PHD finger adopts a globular fold, consisting of a two-stranded beta-sheet and an alpha-helix. The region consisting of these secondary structures and the residues involved in coordinating the zinc-ions are very conserved among species. The loop regions I and II are variable and could contribute functional specificity to the different PHD fingers.
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