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The Plant Homeodomain (PHD) type zinc finger (C4HC3) [1,E1] is found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4-type RING finger. A general function of the PHD finger is not yet known, but in the CREB-binding protein (CBP) it is an integral part of the enzymatic core of the acetyltransferase domain and is also a key contributor to the transcriptional activity of CBP.

The 3D structure of Williams-Beuren Syndrome transcription factor (see <PDB:1F62>) reveals that the PHD finger coordinates two atoms of zinc in a cross-braced manner [2]. This atypical conformation is also shared by the FYVE (see <PDOC50178> and RING fingers (see <PDOC00449>). The two zinc sites are located at opposite ends of a short β-sheet. This feature is also shared by the RING finger and the FYVE domain, but the structure differ in the surrounding loops that vary significantly in length and sequence and could explain the wide variety of functions between these three domains.

Single or multiple PHD fingers are found in the following proteins:

• Drosophila trithorax protein and the homologous mammalian protein HRX (also known as ALL1, MLL and Htrx). The trithorax gene is required for proper regulation of the homeotic genes in flies [3]. The HRX gene is involved in translocations in acute lymphoblastic leukemia. Trithorax has 4 PHD fingers. The most C-terminal one in HRX is degenerated.
• Drosophila Polycomblike, a protein encoded by a Polycomb-group gene. Polycomblike and the Polycomb-group genes are required for correct regulation of the homeotic genes in flies. These genes counteract the effects of the trithorax-group genes presumably by creating an inactive chromatin structure [4]. Polycomblike has 2 PHD fingers.
• Human Xe169 and murine Smcx, proteins encoded by X-linked genes that escape X-chromosome inactivation. Murine Smcy is a related gene on the Y chromo- some. Xe169 has 2 PHD fingers.
• Human RBP2, a Xe169-related protein thought to bind to the Rb protein.
• Human Br140 (also known as peregrin), a protein which also has a bromodomain.
• Medicago sativa Alfin-1, a presumptive transcription factor.
• A group of plant homeobox-containg proteins such as Arabidopsis HAT3 and PRHA, maize ZMHOX1a, parsley PRHP.
• Human Mi-2 autoantigen.
• Drosophila shuttle craft protein.
• Human BS69, a protein that binds adenovirus E1A.
• Murine CBP (CREB-binding protein), the closely related human E1A binding protein p300, and YNJ1, a related protein from C.elegans
• Mammalian zinc-finger protein of the 'requiem' family.
• Human TIF1, a putative transcriptional mediator for nuclear receptors.

The consensus pattern we developped start at the first cysteine and end at the last one, whereas the profile we developed spans the complete domain.

The spacing between cysteines in the PHD finger is closely related to that in the RING finger. Discrimination between these two domains with either a pattern or a profile is therefore difficult, and some rare domains are recognized by both the RING and PHD descriptors.

Aasland R.

May 2002 / First entry.

PROSITE methods (with tools and information) covered by this documentation:

ZF_PHD_2, PS50016; Zinc finger PHD-type profile  (MATRIX)

Sequences known to belong to this class detected by the profile: ALL, except for shuttle craft protein Other sequence(s) detected in Swiss-Prot: NONE.

• Domain architecture view of Swiss-Prot proteins matching PS50016 • Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS50016 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS50016 • Scan Swiss-Prot/TrEMBL entries against PS50016 • view ligand binding statistics

Matching PDB structures: 1F62 1FP0 1MM2 1MM3 ... [ALL]

ZF_PHD_1, PS01359; Zinc finger PHD-type signature  (PATTERN)

Consensus pattern: C-x(1,2)-C-x(5,45)-[VMFLWIE]-x-C-x(1,4)-C-x(1,4)-[WYFVQHLT]-H-x(2)-C-x(5,45)-[WFLYI]-x-C-x(2)-C Sequences known to belong to this class detected by the profile: ALL Other sequence(s) detected in Swiss-Prot: NONE.

• Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS01359 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS01359 • Scan Swiss-Prot/TrEMBL entries against PS01359 • view ligand binding statistics

Matching PDB structures: 1F62 1FP0 1MM2 1MM3 ... [ALL]

1	Authors	Aasland R., Gibson T.J., Stewart A.F.
	Title	The PHD finger: implications for chromatin-mediated transcriptional regulation.
	Source	Trends Biochem. Sci. 20:56-59(1995).
	PubMed ID	7701562

2	Authors	Pascual J., Martinez-Yamout M., Dyson H.J., Wright P.E.
	Title	Structure of the PHD zinc finger from human Williams-Beuren syndrome transcription factor.
	Source	J. Mol. Biol. 304:723-729(2000).
	PubMed ID	11124022
	DOI	10.1006/jmbi.2000.4308

3	Authors	Kennison J.A.
	Title	Transcriptional activation of Drosophila homeotic genes from distant regulatory elements.
	Source	Trends Genet. 9:75-79(1993).
	PubMed ID	8098166

4	Authors	Paro R.
	Title	Mechanisms of heritable gene repression during development of Drosophila.
	Source	Curr. Opin. Cell Biol. 5:999-1005(1993).
	PubMed ID	7907493

E1
Source	http://www.uib.no/aasland/phd/PHD-finger.html

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