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The WDR5 module of
the MLL1 Complex
Akamol (Ake) Klaikherd
7th December 2006
Chromatin
http://en.wikipedia.org/wiki/Histone
Histone Modifications in
Chromatin Regulation
• Histones undergo post translational modification
• Modifications : methylation, acetylation, phosphorylation,
ubiquitination, sumoylation, citrullination, and ADP ribosylation
•Combinations of modifications are thought to constitute a code, the
so-called "histone code".
•Histone modifications act in diverse biological processes such as
gene regulation, DNA repair and chromosome condensation
(mitosis).
Histone Methyltransferase (HMTase)
Histone methyltransferases (HMT)
histone-lysine N-methyltransferase
histone-arginine N-methyltransferase
one to three METHYL groups from the
cofactor s-adenosylmethionine to lysine and
arginine residues of histone proteins.
These proteins often contain an SET (Su(var)3-9, Enhancer of
Zeste, Trithorax) domain.
Trends Genet. 2003, 19, 629-639.
WDR5 in MLL1 Complex
MLL1
WDR5
Characterization of various TRX complexes, such as
mammalian SET1, MLL1 and MLL2, has revealed that
WDR5 is a ubiquitous subunit associated with these SET
domain methyltransferases
An analogous decrease in the global distribution of K4
methylation has been observed in morpholino
knockdowns of WDR5 in Xenopus laevis embryos
The importance of WDR5 are in transcriptional
regulation, particularly of developmentally controlled
genes in metazoans.
Trends Genet. 2003, 19, 629-639.
Histone lysine methylation and disease
tumor
Acute lymphoid leukemia
http://leukemia4111.tripod.com/
Trends Genet. 2003, 19, 629-639.
So?
To understannd the mechanism by which this WDR5 protein
recognizes methylated K4 histone H3
WDR5
WD40 repeat protein
WD40
Cell 2005, 121, 859-827.
WDR5
Cell 2005, 121, 859-827
Recognition of Methylated Histone
H3K4 by the WDR5
Ala
Arg
Thr
Lys
Gln
Hanging-drop vapor-diffusion method
Molecular replacement using MolRep
includes in CCP4
Resolution
Rworking
Rfree
PDB
Mol. Cell 2006, 22, 137-144.
= 1.9 Ao
= 21.2%
= 24.3%
= 2G99
Recognition of Methylated Histone
H3K4 by the WDR5
Arg2
F133
R2
S91
C261
F263
Lys4
E322
D107
Ala1
Mol. Cell 2006, 22, 137-144.
Recognition of Methylated Histone
H3K4 by the WDR5
The hydrogen bonding between dimethylated Lys4 and carboxylate
oxygen of Glu322 in WDR5
The Three amino acid Ala-Arg-Thr preceding Lys4 form most of the
specific contacts with WDR5
Mol. Cell 2006, 22, 137-144.
Molecular Recognition of H3
by the WDR5
WDR5 has been reported to selectively bind dimethylated Lys4 in histone
tp promote K4 trimetylation by TRX (MLL1)
A Homology model was generated using ESypred3D homology modeling
server
Phaser was used as a model for molecular replacement
Resolution
Rworking
Rfree
PDB
WDR5
WDR5-H3
= 1.48 Ao
= 15.7%
= 19.7%
= 2H14
= 1.58 Ao
= 16.6%
= 19.9%
= 2H13
Trievel, RC. et al Nat. Struct. Mol. Biol. 2006, 13, 698-703.
Molecular Recognition of H3
by the WDR5
Trievel, RC. et al Nat. Struct. Mol. Biol. 2006, 13, 698-703.
Molecular Recognition of H3
by the WDR5
Movie!!!
Trievel, RC. et al Nat. Struct. Mol. Biol. 2006, 13, 698-703.
Molecular Recognition of H3
by the WDR5
Trievel, RC. et al Nat. Struct. Mol. Biol. 2006, 13, 698-703.
Structure of WDR5-histone complexes
Verdine, GL. et al Nat. Struct. Mol. Biol. 2006, 13, 704-712.
Structure of WDR5-histone complexes
histone
Verdine, GL. et al Nat. Struct. Mol. Biol. 2006, 13, 704-712.
Refinement Statistics
Apo-WRD5
Resolution (Ao)
Rworking
Rfree
PDB
1.78
17.0
19.2
2H68
Unmodified
H31-15-WDR5
complex
2.25
19.0
22.6
2CO0
H31-9K4me1WDR5 complex
1.89
14.6
19.0
2H6K
H31-9K2me1WDR5 complex
1.50
17.9
19.8
2H6N
H31-9K4me3WDR5 complex
1.88
15.2
18.5
2H6Q
Hanging-drop vapor-diffusion method
Molecular replacement using
MOLREP and BREAST from CCP4
suite
Verdine, GL. et al Nat. Struct. Mol. Biol. 2006, 13, 704-712.
Histone H3 Peptide Recognition
Verdine, GL. et al Nat. Struct. Mol. Biol. 2006, 13, 704-712.
Histone H3 Peptide Recognition
Phe149
Arg2
Phe133
Phe263
Apo-WDR5
H3K4me2
Verdine, GL. et al Nat. Struct. Mol. Biol. 2006, 13, 704-712.
Movie
Summary
Summary
WDR5 preferentially binds Ala-Arg-Thr in N-terminus of Histone H3
peptide
WDR5 does not directly interact with Lys4.
Methylation state of Lys4 does not affect histone H3 recognition
References:
Chai, J. Mol. Cell 2006, 22, 137-144.
Trievel, RC. et al Nat. Struct. Mol. Biol. 2006, 13, 698-703.
Verdine, GL. et al Nat. Struct. Mol. Biol. 2006, 13, 704-712.