PDBsum entry 3gl6

Oxidoreductase

PDB id: 3gl6

Contents

Protein chain

52 a.a. *

Ligands

ALA-ARG-THR-M3L-GLN-THR-ALA-ARG

Metals

_ZN ×3

Waters ×32

* Residue conservation analysis

PDB id:

3gl6

Name:

Oxidoreductase

Title:

Crystal structure of jarid1a-phd3 complexed with h3(1-9)k4me3 peptide

Structure:

Histone demethylase jarid1a. Chain: a. Fragment: c-terminal phd finger. Synonym: jumonji/arid domain-containing protein 1a, retinoblastoma- binding protein 2, rbbp-2. Engineered: yes. Histone h3. Chain: b. Fragment: histone h3 n-terminal residues 1-9.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: jarid1a, rbbp2, rbp2. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 9606

Resolution:

1.90Å R-factor: 0.208 R-free: 0.225

Authors:

Z.Wang,J.Song,D.J.Patel

Key ref:

G.G.Wang et al. (2009). Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger. Nature, 459, 847-851. PubMed id: 19430464 DOI: 10.1038/nature08036

Date:

11-Mar-09 Release date: 05-May-09

Protein chain

P29375  (KDM5A_HUMAN) -  Lysine-specific demethylase 5A from Homo sapiens

Seq: 1690 a.a.

Struc: 52 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.14.11.67 - [histone H3]-trimethyl-L-lysine(4) demethylase.
• Reaction: N₆,N₆,N₆-trimethyl-L-lysyl₄-[histone H3] + 3 2-oxoglutarate + 3 O2 = L-lysyl₄-[histone H3] + 3 formaldehyde + 3 succinate + 3 CO2

N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3] + 3 × 2-oxoglutarate (Bound ligand (Het Group name = GLN) matches with 58.33% similarity) + 3 × O2 = L-lysyl(4)-[histone H3] + 3 × formaldehyde (Bound ligand (Het Group name = ALA) matches with 40.00% similarity) + 3 × succinate (Bound ligand (Het Group name = THR) matches with 50.00% similarity) + 3 × CO2

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nature08036

Nature 459:847-851 (2009)

PubMed id: 19430464

Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger.

G.G.Wang, J.Song, Z.Wang, H.L.Dormann, F.Casadio, H.Li, J.L.Luo, D.J.Patel, C.D.Allis.

ABSTRACT

Histone H3 lysine 4 methylation (H3K4me) has been proposed as a critical component in regulating gene expression, epigenetic states, and cellular identities1. The biological meaning of H3K4me is interpreted by conserved modules including plant homeodomain (PHD) fingers that recognize varied H3K4me states. The dysregulation of PHD fingers has been implicated in several human diseases, including cancers and immune or neurological disorders. Here we report that fusing an H3K4-trimethylation (H3K4me3)-binding PHD finger, such as the carboxy-terminal PHD finger of PHF23 or JARID1A (also known as KDM5A or RBBP2), to a common fusion partner nucleoporin-98 (NUP98) as identified in human leukaemias, generated potent oncoproteins that arrested haematopoietic differentiation and induced acute myeloid leukaemia in murine models. In these processes, a PHD finger that specifically recognizes H3K4me3/2 marks was essential for leukaemogenesis. Mutations in PHD fingers that abrogated H3K4me3 binding also abolished leukaemic transformation. NUP98-PHD fusion prevented the differentiation-associated removal of H3K4me3 at many loci encoding lineage-specific transcription factors (Hox(s), Gata3, Meis1, Eya1 and Pbx1), and enforced their active gene transcription in murine haematopoietic stem/progenitor cells. Mechanistically, NUP98-PHD fusions act as 'chromatin boundary factors', dominating over polycomb-mediated gene silencing to 'lock' developmentally critical loci into an active chromatin state (H3K4me3 with induced histone acetylation), a state that defined leukaemia stem cells. Collectively, our studies represent, to our knowledge, the first report that deregulation of the PHD finger, an 'effector' of specific histone modification, perturbs the epigenetic dynamics on developmentally critical loci, catastrophizes cellular fate decision-making, and even causes oncogenesis during mammalian development.

Selected figure(s)

Figure 2.
Figure 2: JARID1A-PHD3, an essential motif for NJL-mediated leukaemia, specifically recognizes H3K4me3/2 marks. a, Capability of JARID1A-PHD3, PHF23-PHD and JARID1A-PHD1 (the first PHD finger of JARID1A; Supplementary Fig. 1) to interact with H3 peptides containing different states of Lys methylation, in a peptide pull-down assay. JARID1A-PHD1 interacted with H3K4me0 as BHC80-PHD^11. aa, amino acids. b, The crystal structure of JARID1A-PHD3 (cyan) complexed with H3K4me3 peptide (yellow), and a close-up view of the H3K4me3-binding channel (inset) formed by two orthogonally aligned Trp residues. The numeration of JARID1A-PHD3 and H3 residues is shown in red and black, respectively. Protein Data Bank accession number, 3GL6. c, Capability of wild-type (WT) or mutant JARID1A-PHD3 to bind to H3K4me3/2. d, Co-immunoprecipitation showing that NJL containing the wild-type, but not mutant (W1625A) PHD finger, associated with H3K4me3 or H3 in transiently transfected 293 cells.

Figure 4.
Figure 4: The H3K4me3/2 engagement by NUP98–JARID1A perturbs the epigenetic state of developmentally critical loci during haematopoiesis. a, The impact of mutations on Flag–NJL binding to HOXA9 in 293 cells. WT, wild type. b, Immunoblot of haematopoietic progenitors 10 days after transduction of vector, wild-type or mutant NJL. Phosphorylated c-Kit (P-c-Kit) is a marker of mast cells. Actin is shown as a loading control. c, ChIP for Hoxa9 promoter-associated NUP98-fusion proteins (3 Flag-tagged) and H3K4me3 in marrow progenitors 10 days after transduction. d, e, Transforming capacities after introducing mutation to NJL (d) or those by NUP98–PHF23 (e) or after replacing JARID1A-PHD3 with another PHD finger that engages either H3K4me3/2 or H3K4me0. The total progenitor number was counted at day 1, 10, 25 and 40. f–h ChIP for Suz12 (f), Mll2-binding to Hoxa9/a11 (g), and Hoxa9-associated H3 acetylation (h) in marrow progenitors 15 days after transduction of vector or NJL. Error bar indicates s.d.; n = 3; *P < 0.05, **P < 0.005, ***P < 10^-4 and *****P < 10^-6. i, A scheme showing that NUP98–PHD fusion acts as a boundary factor and prevents the spreading of polycomb factors from Hoxa13/a11 to Hoxa9, thus inhibiting H3K4me3 removal and H3K27me3 addition during haematopoiesis.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nature (2009, 459, 847-851) copyright 2009.

Figures were selected by an automated process.