PDBsum entry 3kqi

Nuclear protein

PDB id

3kqi

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Contents

			Protein chain

					71 a.a. *

			Ligands

					ALA-ARG-THR-M3L- GLN-THR


					GOL

			Metals

					_MG ×2


					_ZN ×2


					_CL

			Waters ×125

* Residue conservation analysis

PDB id:

3kqi

Links

Name:

Nuclear protein

Title:

Crystal structure of phf2 phd domain complexed with h3k4me3 peptide

Structure:

Phd finger protein 2. Chain: a. Fragment: phd finger. Synonym: grc5. Engineered: yes. H3k4me3 peptide. Chain: b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: kiaa0662, phf2. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes

Resolution:

1.78Å

R-factor:

0.191

R-free:

0.218

Authors:

H.Wen,J.Z.Li,T.Song,M.Lu,M.Lee

Key ref:

H.Wen et al. (2010). Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation. J Biol Chem, 285, 9322-9326. PubMed id: 20129925

Date:

17-Nov-09

Release date:

02-Feb-10

PROCHECK

	Headers

	References

Protein chain

O75151 (PHF2_HUMAN) - Lysine-specific demethylase PHF2 from Homo sapiens

Seq: Struc:

Seq: Struc:

Seq: Struc:					1096 a.a. 71 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.1.14.11.- - ?????

[IntEnz] [ExPASy] [KEGG] [BRENDA]

	J Biol Chem 285:9322-9326 (2010)
PubMed id: 20129925

Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation.
H.Wen, J.Li, T.Song, M.Lu, P.Y.Kan, M.G.Lee, B.Sha, X.Shi.

ABSTRACT

Distinct lysine methylation marks on histones create dynamic signatures deciphered by the "effector" modules, although the underlying mechanisms remain unclear. We identified the plant homeodomain- and Jumonji C domain-containing protein PHF2 as a novel histone H3K9 demethylase. We show in biochemical and crystallographic analyses that PHF2 recognizes histone H3K4 trimethylation through its plant homeodomain finger and that this interaction is essential for PHF2 occupancy and H3K9 demethylation at rDNA promoters. Our study provides molecular insights into the mechanism by which distinct effector domains within a protein cooperatively modulate the "cross-talk" of histone modifications.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20818169

K.Fortschegger, and R.Shiekhattar (2011).
Plant homeodomain fingers form a helping hand for transcription.

Epigenetics, 6, 4-8.

21059680

P.Slama, and D.Geman (2011).
Identification of family-determining residues in PHD fingers.

Nucleic Acids Res, 39, 1666-1679.

21243712

P.Voigt, and D.Reinberg (2011).
Histone tails: ideal motifs for probing epigenetics through chemical biology approaches.

Chembiochem, 12, 236-252.

20548336

J.Qiu, G.Shi, Y.Jia, J.Li, M.Wu, J.Li, S.Dong, and J.Wong (2010).
The X-linked mental retardation gene PHF8 is a histone demethylase involved in neuronal differentiation.

Cell Res, 20, 908-918.

20923397

K.L.Yap, and M.M.Zhou (2010).
Keeping it in the family: diverse histone recognition by conserved structural folds.

Crit Rev Biochem Mol Biol, 45, 488-505.

20953165

R.A.Varier, N.S.Outchkourov, P.de Graaf, F.M.van Schaik, H.J.Ensing, F.Wang, J.M.Higgins, G.J.Kops, and H.T.Timmers (2010).
A phospho/methyl switch at histone H3 regulates TFIID association with mitotic chromosomes.

EMBO J, 29, 3967-3978.

20813266

S.Ohta, J.C.Bukowski-Wills, L.Sanchez-Pulido, F.d.e. .L.Alves, L.Wood, Z.A.Chen, M.Platani, L.Fischer, D.F.Hudson, C.P.Ponting, T.Fukagawa, W.C.Earnshaw, and J.Rappsilber (2010).
The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics.

Cell, 142, 810-821.

20531378

Z.Zhu, Y.Wang, X.Li, Y.Wang, L.Xu, X.Wang, T.Sun, X.Dong, L.Chen, H.Mao, Y.Yu, J.Li, J.Li, P.A.Chen, and C.D.Chen (2010).
PHF8 is a histone H3K9me2 demethylase regulating rRNA synthesis.

Cell Res, 20, 794-801.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.