PHD3 reading H3K4me3: Kd 4.3 uM for the PHD3-bromo cassette, 30 uM for PHD3 alone, two co-crystals - and the whole module is thrown away by the breakpoint
also called MLL1 PHD3-Bromo · H3K4me3 reader · 3LQJ · 3LQI
Normal KMT2A can read the very histone mark it writes, through a small finger near its middle, and the neighbouring bromodomain makes that reading about seven times better. The leukaemic fusion is cut before the finger and cannot read anything.
The same thing, for a scientist
KMT2A's third PHD finger binds H3K4me3 preferentially over lower methylation states, and it does so in cis with the adjacent bromodomain. ITC on the coexpressed PHD3-bromo cassette gives Kd 4.3 uM for H3K4me3, 6.9 uM for H3K4me2 and 53 uM for H3K4me1; PHD3 alone binds H3K4me3 at about 30 uM, so the bromodomain contributes roughly sevenfold. The crystallised cassette is PDB 3LQJ (1.90 A, H3K4me3) and 3LQI (1.92 A, H3K4me2), with the free form at 3LQH (1.72 A); the isolated PHD3 solution structure 2KYU maps to Q03164 1564-1628 against the fetched UniProt sequence. W1594 is the aromatic-cage tryptophan required for methyl-lysine recognition: W1594A impairs H3K4me3 binding while leaving CyP33 RRM affinity essentially intact. The entire PHD1-3-bromodomain cassette lies C-terminal to the breakpoint cluster region and is absent from every leukaemogenic KMT2A fusion.
Two labs, two numbers, one module
| construct | ligand | Kd | source |
|---|---|---|---|
| PHD3-bromo cassette | H3K4me3 | 4.3 uM | Wang et al. 1 |
| PHD3-bromo cassette | H3K4me2 | 6.9 uM | Wang et al. 1 |
| PHD3-bromo cassette | H3K4me1 | 53 uM | Wang et al. 1 |
| PHD3 alone | H3K4me3 | ~30 uM | Park et al. 2 |
| PHD3 W1594A | H3K4me3 | impaired | Park et al. 2 |
| PHD3 V1617A | H3K4me3 | 52.4 uM (1.7x weaker) | Park et al. 2 |
The two studies were published within months of each other and agree on the essentials: PHD3 prefers trimethyl, the bromodomain adds affinity, and the aromatic cage tryptophan is W1594. They disagree on something else, which is the subject of the companion entry interface-kmt2a-phd3-cyp33-rrm.
A reader lost, in a protein defined by what it writes
The UniProt-mapped PHD3 span 1564-1628 sits C-terminal to the KMT2A breakpoint cluster region, so the fusion has no H3K4me3 reader. That matters more than a generic domain loss: it means the fusion cannot execute the read-write feedback that normally couples MLL1's product to its own residence. The graph's mechanism-phd3-cyp33-repressor-switch-lost and localization-phd-cluster-1416-1640-is-lost-ten-residues-past-the-junction carry the functional and positional accounts; what was missing was the affinity and the reader residue, which are here.
| partner a | gene-kmt2a |
|---|---|
| partner b | histone H3 K4me3 |
| motif a | KMT2A PHD3 finger, mapped to Q03164 1564-1628, acting with the adjacent bromodomain as a PHD3-bromo cassette |
| motif b | histone H3 N-terminal tail, residues 1-9, trimethylated at K4 |
| kd NM | 4300 |
| fate in fusion | lost - PHD3 at 1564-1628 lies C-terminal to the breakpoint cluster region and is absent from every leukaemogenic KMT2A fusion |
| druggability | a methyl-lysine aromatic cage plus an adjacent bromodomain; bromodomains are a well-precedented small-molecule class, but the module is absent from the fusion, so this is wild-type-allele chemistry |
| resolution note | PDB metadata and entity sequences fetched from data.rcsb.org 2026-09-20; PHD3 span aligned to UniProt Q03164 fetched the same day |
interface residues a
[ "KMT2A W1594 (aromatic cage tryptophan)", "KMT2A Q1587 (reporter amide in NMR titration)" ]
kd measurements — the numbers behind the chart
[
{
"ligand": "PHD3-bromo cassette + H3K4me3",
"kd_nM": 4300,
"method": "ITC",
"source_pmid": "20541251"
},
{
"ligand": "PHD3-bromo cassette + H3K4me2",
"kd_nM": 6900,
"method": "ITC",
"source_pmid": "20541251"
},
{
"ligand": "PHD3-bromo cassette + H3K4me1",
"kd_nM": 53000,
"method": "ITC",
"source_pmid": "20541251"
},
{
"ligand": "PHD3 alone + H3K4me3",
"kd_nM": 30000,
"method": "ITC",
"source_pmid": "20677832"
},
{
"ligand": "PHD3 V1617A + H3K4me3",
"kd_nM": 52400,
"method": "ITC",
"source_pmid": "20677832"
}
]structures
[ "3LQJ", "3LQI", "3LQH", "2KYU" ]
structure details — the numbers behind the chart
[
{
"pdb": "3LQJ",
"title_fetched": "Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me3 peptide",
"method": "X-ray",
"resolution_A": 1.9,
"fetched": "2026-09-20"
},
{
"pdb": "3LQI",
"title_fetched": "Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide",
"method": "X-ray",
"resolution_A": 1.92,
"fetched": "2026-09-20"
},
{
"pdb": "3LQH",
"title_fetched": "Crystal structure of MLL1 PHD3-Bromo in the free form",
"method": "X-ray",
"resolution_A": 1.72,
"fetched": "2026-09-20"
},
{
"pdb": "2KYU",
"title_fetched": "The solution structure of the PHD3 finger of MLL",
"method": "NMR",
"resolution_A": null,
"contents": "Q03164 1564-1628",
"fetched": "2026-09-20"
}
]- Wrong allele: the module is not in the fusion, so any PHD3 or bromodomain ligand acts on wild-type MLL1.
- Reader redundancy: many proteins read H3K4me3, so removing one micromolar reader from one complex may change nothing measurable.
- Weak affinity: a 4.3 uM reader is easily out-competed, which cuts both ways - it is a poor target and a poor lever.
- Cassette coupling: PHD3 and the bromodomain communicate through a linker proline whose isomerisation state is enzyme-controlled, so a ligand for one may behave differently depending on CyP33 activity.
- Does re-inserting PHD3 into a fusion restore H3K4me3 reading measurably, or does it block transformation through the CyP33 arm alone? The two functions are separable by W1594A and V1617A and this has never been tested in a fusion context.
- At 4.3 uM, is the PHD3-bromo cassette ever appreciably occupied at physiological H3K4me3 density, or does it require nucleosome-level avidity the peptide assays cannot see?
- Is the bromodomain of the cassette a genuine acetyl-lysine reader in cis, and does it have its own ligand?
- E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
The MLL1 PHD3-bromodomain cassette binds H3K4me3 at Kd 4.3 uM, H3K4me2 at 6.9 uM and H3K4me1 at 53 uM by ITC, and PHD3 alone binds H3K4me peptides much more weakly.
Pro isomerization in MLL1 PHD3-bromo cassette connects H3K4me readout to CyP33 and HDAC-mediated repression. · Wang Z, Song J, Milne TA, et al. · Cell 2010What this evidence cannot show
ITC on H3(1-15) peptides and a coexpressed cassette; all affinities are micromolar, which for a chromatin reader is ordinary but means occupancy depends heavily on local mark density. The comparison to PHD3 alone is relegated to a supplementary table in the source. Full text reached by efetch db=pmc after fullTextXML returned HTTP 500.
Evidence that argues against this (1)
- Park et al. measure PHD3 alone at about 30 uM for H3K4me3, which is only sevenfold weaker than the cassette, so the bromodomain's contribution is real but modest and the two studies imply somewhat different pictures of how much the cassette matters. Park S et al. 2010
- E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
MLL PHD3 binds H3K4me3 with 1:1 stoichiometry at Kd about 30 uM by ITC; W1594A impairs H3K4me3 binding without materially changing CyP33 RRM affinity (19.6 uM against 14.7 uM wild type), and V1617A weakens H3K4me3 binding only 1.7-fold to 52.4 uM.
The PHD3 domain of MLL acts as a CYP33-regulated switch between MLL-mediated activation and repression . · Park S, Osmers U, Raman G, et al. · Biochemistry 2010What this evidence cannot show
Isolated PHD3 domain without the bromodomain, so the numbers are not directly comparable to the cassette values; mutational separation of the two surfaces is the paper's central claim and rests on two point mutants.
Evidence that argues against this (1)
- Wang et al. show the bromodomain packs against PHD3 and that a linker proline isomerisation reorganises the cassette, so an isolated PHD3 may present a surface the intact cassette does not. Wang Z et al. 2010
- E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
PDB 3LQJ is a 1.90 A crystal of the MLL1 PHD3-bromo cassette with an H3(1-9)K4me3 peptide; 3LQI is the 1.92 A H3K4me2 complex and 2KYU is the isolated PHD3 solution structure mapping to Q03164 1564-1628.
PDB 3LQJ: Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me3 peptide · Wang Z, Song J, Milne TA, et al. · RCSB Protein Data Bank 2010What this evidence cannot show
Titles, methods, resolutions and entity sequences fetched from data.rcsb.org 2026-09-20; the PHD3 span is this cycle's alignment to the UniProt Q03164 sequence fetched the same day, after stripping the GS expression tag. The histone ligand is a 9-residue peptide, not a nucleosome.
Evidence that argues against this (1)
- A 9-residue histone peptide cannot report on nucleosome-level avidity or on competition with other H3K4me3 readers present in the same nucleus. Park S et al. 2010
PHD3 1564-1628 reads H3K4me3, Kd 4.3 uM with the bromodomain
supplies the reader affinity and the aromatic-cage residue that entry lacked
structural coordinates for the lost cassette
- supports →Lost from the KMT2A half: PHD3 and the bromodomain are one cassette, not two modules (aa 1566-1765)
affinity and residue detail for the subtracted module
- related to →KMT2A::AFF1 (MLL-AF4), t(4;11)(q21;q23)
absent from the index fusion
the competing or coexisting ligand on the same finger
the same mark menin raises at TFF1 as at HOXA9
the mark that interface binds - previously a forward reference with no node behind it
a competing PHD-finger reader of the same mark, with the opposite transcriptional output
KMT2A's PHD1-3/bromo cassette (Q03164 aa 1431-1765) is the homologue of the module the H4R3 gate acts on in KMT2D - and it is lost from every 5'-KMT2A fusion; whether it reads H4R3 is untested