Tudor domain of PHD finger protein 1

The TUDOR domain is a 5-stranded beta-barrel protein, colored light green. It binds to trimethylated Lys36 of Histone 3, shown in CPK colors. The Lys36 fits into one end of the barrel, between two loops.


Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1.
Musselman CA, Avvakumov N, Watanabe R, Abraham CG, Lalonde ME, Hong Z, Allen C, Roy S, Nuñez JK, Nickoloff J, Kulesza CA, Yasui A, Côté J, Kutateladze TG.
Nat Struct Mol Biol. 2012 Dec;19(12):1266-72

(PubMed)

4hcz (PDB)

 

Tudor: a versatile family of histone methylation 'readers'.
Lu R, Wang GG.
Trends Biochem Sci. 2013 Nov;38(11):546-55. doi: 10.1016/j.tibs.2013.08.002. Epub 2013 Sep 10. Review.
Free PMC Article

Abstract
The Tudor domain comprises a family of motifs that mediate protein-protein interactions required for various DNA-templated biological processes. Emerging evidence demonstrates a versatility of the Tudor family domains by identifying their specific interactions to a wide variety of histone methylation marks. Here, we discuss novel functions of a number of Tudor-containing proteins [including Jumonji domain-containing 2A (JMJD2A), p53-binding protein 1 (53BP1), SAGA-associated factor 29 (SGF29), Spindlin1, ubiquitin-like with PHD and RING finger domains 1 (UHRF1), PHD finger protein 1 (PHF1), PHD finger protein 19 (PHF19), and SAWADEE homeodomain homolog 1 (SHH1)] in 'reading' unique methylation events on histones in order to facilitate DNA damage repair or regulate transcription. This review covers our recent understanding of the molecular bases for histone-Tudor interactions and their biological outcomes. As deregulation of Tudor-containing proteins is associated with certain human disorders, pharmacological targeting of Tudor interactions could provide new avenues for therapeutic intervention.

The PHD finger: a versatile epigenome reader.
Sanchez R, Zhou MM.
Trends Biochem Sci. 2011 Jul;36(7):364-72. doi: 10.1016/j.tibs.2011.03.005. Epub 2011 Apr 21. Review.


Free PMC Article

Abstract
PHD (plant homeodomain) zinc fingers are structurally conserved modules found in proteins that modify chromatin as well as mediate molecular interactions in gene transcription. The original discovery of their role in gene transcription is attributed to the recognition of lysine-methylated histone H3. Recent studies show that PHD fingers have a sophisticated histone sequence reading capacity that is modulated by the interplay between different histone modifications. These studies underscore the functional versatility of PHD fingers as epigenome readers that control gene expression through molecular recruitment of multiprotein complexes of chromatin regulators and transcription factors. Moreover, they reinforce the concept that evolutionary changes in amino acids surrounding ligand binding sites on a conserved structural fold impart great functional diversity upon this family of proteins.