ISDA

Deposition Date 2009-10-29

Release Date 2009-11-17

Last Version Date 2023-12-20

Entry Detail

PDB ID:

2WWU

Keywords:

METAL BINDING PROTEIN

Title:

Crystal structure of the catalytic domain of PHD finger protein 8

Biological Source:

Source Organism:

HOMO SAPIENS (Taxon ID: 9606)

Host Organism:

ESCHERICHIA COLI

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.15 Å

R-Value Free:

0.21

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

I 21 3

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PHD FINGER PROTEIN 8
Gene (Uniprot):PHF8
Chain IDs:A
Chain Length:371
Number of Molecules:1
Biological Source:HOMO SAPIENS

UniProt ID:Q9UPP1 Pfam ID:PF02373, PF17811 EC:1.14.11.65

Ligand Molecules

ACT

BGC

SO4

Primary Citation

Crystal structure of the PHF8 Jumonji domain, an Nepsilon-methyl lysine demethylase.

Yue, W.W, Hozjan, V, Ge, W, Loenarz, C, Cooper, C.D, Schofield, C.J, Kavanagh, K.L, Oppermann, U, McDonough, M.A.Show

FEBS Lett. 584 825 830 (2010)

PMID: 20067792 DOI: 10.1016/j.febslet.2009.12.055

Abstact

Crystallographic analysis of the catalytic domain of PHD finger protein 8 (PHF8), an N(epsilon)-methyl lysine histone demethylase associated with mental retardation and cleft lip/palate, reveals a double-stranded beta-helix fold with conserved Fe(II) and cosubstrate binding sites typical of the 2-oxoglutarate dependent oxygenases. The PHF8 active site is highly conserved with those of the FBXL10/11demethylases, which are also selective for the di-/mono-methylated lysine states, but differs from that of the JMJD2 demethylases which are selective for tri-/di-methylated states. The results rationalize the lack of activity for the clinically observed F279S PHF8 variant and they will help to identify inhibitors selective for specific N(epsilon)-methyl lysine demethylase subfamilies.

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Primary Citation of related structures