 |
PDBsum entry 2rje
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Transcription
|
PDB id
|
|
|
|
2rje
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Transcription
|
|
|
Title:
|
|
Crystal structure of l3mbtl1 in complex with h4k20me2 (residues 17- 25), orthorhombic form ii
|
|
Structure:
|
|
Lethal(3)malignant brain tumor-like protein. Chain: a, b, c. Fragment: residues 200-530. Synonym: l(3)mbt-like, l(3)mbt protein homolog, h-l(3)mbt protein, h- l(3)mbt, l3mbtl1. Engineered: yes. Histone h4. Chain: p, q. Engineered: yes
|
|
Source:
|
|
Homo sapiens. Human. Organism_taxid: 9606. Gene: l3mbtl, kiaa0681, l3mbt. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: synthetic peptide
|
|
Resolution:
|
|
|
1.86Å
|
R-factor:
|
0.193
|
R-free:
|
0.231
|
|
|
Authors:
|
|
A.Allali-Hassani,Y.Liu,N.Herzanych,H.Ouyang,F.Mackenzie,L.Crombet, P.Loppnau,I.Kozieradzki,M.Vedadi,J.Weigelt,M.Sundstrom, C.H.Arrowsmith,A.M.Edwards,A.Bochkarev,J.R.Min,Structural Genomics Consortium (Sgc)
|
Key ref:
|
|
J.Min
et al.
(2007).
L3MBTL1 recognition of mono- and dimethylated histones.
Nat Struct Biol,
14,
1229-1230.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
14-Oct-07
|
Release date:
|
30-Oct-07
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
Q9Y468
(LMBL1_HUMAN) -
Lethal(3)malignant brain tumor-like protein 1 from Homo sapiens
|
|
|
|
Seq:
Struc:
|
|
|
|
840 a.a.
309 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Key: |
 |
PfamA domain |
|
|
 |
Secondary structure |
|
 |
CATH domain |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Nat Struct Biol
14:1229-1230
(2007)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
L3MBTL1 recognition of mono- and dimethylated histones.
|
|
J.Min,
A.Allali-Hassani,
N.Nady,
C.Qi,
H.Ouyang,
Y.Liu,
F.MacKenzie,
M.Vedadi,
C.H.Arrowsmith.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Crystal structures of the L3MBTL1 MBT repeats in complex with histone H4
peptides dimethylated on Lys20 (H4K20me2) show that only the second of the three
MBT repeats can bind mono- and dimethylated histone peptides. Its binding pocket
has similarities to that of 53BP1 and is able to recognize the degree of histone
lysine methylation. An unexpected mode of peptide-mediated dimerization suggests
a possible mechanism for chromatin compaction by L3MBTL1.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
Figure 1.
(a) Structure of 3MBT bound to an H4K20me2 peptide (residues
17–25). H4K20me2 peptide is shown in red and the
dimethyllysine is shown as a stick model. (b) Sequence alignment
of MBT2, MBT1 and MBT3. Red, identical; blue, conserved; dots,
lysine-binding pocket residues. (c) Superimposition of the three
MBT repeats in 3MBT. Residues forming the lysine-binding pocket
are shown as green sticks, and Phe256 from MBT1 and Arg467 from
MBT3 are colored pink and blue, respectively. H4K20me2 peptide
is shown as yellow sticks.
|
|
Figure 2.
(a,b) 3MBT (a, green backbone) and 53BP1 (b, gray backbone).
Lysine-binding pocket residues and H4K20me2 peptide are shown as
stick models.
|
|
|
|
|
|
| |
The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2007,
14,
1229-1230)
copyright 2007.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
C.A.Musselman,
M.E.Lalonde,
J.Côté,
and
T.G.Kutateladze
(2012).
Perceiving the epigenetic landscape through histone readers.
|
| |
Nat Struct Mol Biol,
19,
1218-1227.
|
|
|
|
|
|
|
C.Xu,
and
J.Min
(2011).
Structure and function of WD40 domain proteins.
|
| |
Protein Cell,
2,
202-214.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
H.Honda,
K.Takubo,
H.Oda,
K.Kosaki,
T.Tazaki,
N.Yamasaki,
K.Miyazaki,
K.A.Moore,
Z.Honda,
T.Suda,
and
I.R.Lemischka
(2011).
Hemp, an mbt domain-containing protein, plays essential roles in hematopoietic stem cell function and skeletal formation.
|
| |
Proc Natl Acad Sci U S A,
108,
2468-2473.
|
|
|
|
|
|
|
K.Acs,
M.S.Luijsterburg,
L.Ackermann,
F.A.Salomons,
T.Hoppe,
and
N.P.Dantuma
(2011).
The AAA-ATPase VCP/p97 promotes 53BP1 recruitment by removing L3MBTL1 from DNA double-strand breaks.
|
| |
Nat Struct Mol Biol,
18,
1345-1350.
|
|
|
|
|
|
|
P.Voigt,
and
D.Reinberg
(2011).
Histone tails: ideal motifs for probing epigenetics through chemical biology approaches.
|
| |
Chembiochem,
12,
236-252.
|
|
|
|
|
|
|
C.Xu,
C.Bian,
W.Yang,
M.Galka,
H.Ouyang,
C.Chen,
W.Qiu,
H.Liu,
A.E.Jones,
F.MacKenzie,
P.Pan,
S.S.Li,
H.Wang,
and
J.Min
(2010).
Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2).
|
| |
Proc Natl Acad Sci U S A,
107,
19266-19271.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
K.Liu,
C.Chen,
Y.Guo,
R.Lam,
C.Bian,
C.Xu,
D.Y.Zhao,
J.Jin,
F.MacKenzie,
T.Pawson,
and
J.Min
(2010).
Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain.
|
| |
Proc Natl Acad Sci U S A,
107,
18398-18403.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
L.Addou-Klouche,
J.Adélaïde,
P.Finetti,
N.Cervera,
A.Ferrari,
I.Bekhouche,
F.Sircoulomb,
C.Sotiriou,
P.Viens,
S.Moulessehoul,
F.Bertucci,
D.Birnbaum,
and
M.Chaffanet
(2010).
Loss, mutation and deregulation of L3MBTL4 in breast cancers.
|
| |
Mol Cancer,
9,
213.
|
|
|
|
|
|
|
L.Balakrishnan,
and
B.Milavetz
(2010).
Decoding the histone H4 lysine 20 methylation mark.
|
| |
Crit Rev Biochem Mol Biol,
45,
440-452.
|
|
|
|
|
|
|
L.M.Congdon,
S.I.Houston,
C.S.Veerappan,
T.M.Spektor,
and
J.C.Rice
(2010).
PR-Set7-mediated monomethylation of histone H4 lysine 20 at specific genomic regions induces transcriptional repression.
|
| |
J Cell Biochem,
110,
609-619.
|
|
|
|
|
|
|
M.A.Adams-Cioaba,
Y.Guo,
C.Bian,
M.F.Amaya,
R.Lam,
G.A.Wasney,
M.Vedadi,
C.Xu,
and
J.Min
(2010).
Structural studies of the tandem Tudor domains of fragile X mental retardation related proteins FXR1 and FXR2.
|
| |
PLoS One,
5,
e13559.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Vedadi,
C.H.Arrowsmith,
A.Allali-Hassani,
G.Senisterra,
and
G.A.Wasney
(2010).
Biophysical characterization of recombinant proteins: a key to higher structural genomics success.
|
| |
J Struct Biol,
172,
107-119.
|
|
|
|
|
|
|
N.Gurvich,
F.Perna,
A.Farina,
F.Voza,
S.Menendez,
J.Hurwitz,
and
S.D.Nimer
(2010).
L3MBTL1 polycomb protein, a candidate tumor suppressor in del(20q12) myeloid disorders, is essential for genome stability.
|
| |
Proc Natl Acad Sci U S A,
107,
22552-22557.
|
|
|
|
|
|
|
W.P.Janzen,
T.J.Wigle,
J.Jin,
and
S.V.Frye
(2010).
Epigenetics: Tools and Technologies.
|
| |
Drug Discov Today Technol,
7,
e59-e65.
|
|
|
|
|
|
|
C.A.Musselman,
and
T.G.Kutateladze
(2009).
PHD fingers: epigenetic effectors and potential drug targets.
|
| |
Mol Interv,
9,
314-323.
|
|
|
|
|
|
|
C.Grimm,
R.Matos,
N.Ly-Hartig,
U.Steuerwald,
D.Lindner,
V.Rybin,
J.Müller,
and
C.W.Müller
(2009).
Molecular recognition of histone lysine methylation by the Polycomb group repressor dSfmbt.
|
| |
EMBO J,
28,
1965-1977.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
F.Liu,
X.Chen,
A.Allali-Hassani,
A.M.Quinn,
G.A.Wasney,
A.Dong,
D.Barsyte,
I.Kozieradzki,
G.Senisterra,
I.Chau,
A.Siarheyeva,
D.B.Kireev,
A.Jadhav,
J.M.Herold,
S.V.Frye,
C.H.Arrowsmith,
P.J.Brown,
A.Simeonov,
M.Vedadi,
and
J.Jin
(2009).
Discovery of a 2,4-diamino-7-aminoalkoxyquinazoline as a potent and selective inhibitor of histone lysine methyltransferase G9a.
|
| |
J Med Chem,
52,
7950-7953.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Eryilmaz,
P.Pan,
M.F.Amaya,
A.Allali-Hassani,
A.Dong,
M.A.Adams-Cioaba,
F.Mackenzie,
M.Vedadi,
and
J.Min
(2009).
Structural studies of a four-MBT repeat protein MBTD1.
|
| |
PLoS One,
4,
e7274.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.S.Champagne,
and
T.G.Kutateladze
(2009).
Structural insight into histone recognition by the ING PHD fingers.
|
| |
Curr Drug Targets,
10,
432-441.
|
|
|
|
|
|
|
M.A.Adams-Cioaba,
and
J.Min
(2009).
Structure and function of histone methylation binding proteins.
|
| |
Biochem Cell Biol,
87,
93.
|
|
|
|
|
|
|
M.J.Hitchler,
and
F.E.Domann
(2009).
Metabolic defects provide a spark for the epigenetic switch in cancer.
|
| |
Free Radic Biol Med,
47,
115-127.
|
|
|
|
|
|
|
P.V.Peña,
C.A.Musselman,
A.J.Kuo,
O.Gozani,
and
T.G.Kutateladze
(2009).
NMR assignments and histone specificity of the ING2 PHD finger.
|
| |
Magn Reson Chem,
47,
352-358.
|
|
|
|
|
|
|
S.S.Ng,
W.W.Yue,
U.Oppermann,
and
R.J.Klose
(2009).
Dynamic protein methylation in chromatin biology.
|
| |
Cell Mol Life Sci,
66,
407-422.
|
|
|
|
|
|
|
Y.Guo,
N.Nady,
C.Qi,
A.Allali-Hassani,
H.Zhu,
P.Pan,
M.A.Adams-Cioaba,
M.F.Amaya,
A.Dong,
M.Vedadi,
M.Schapira,
R.J.Read,
C.H.Arrowsmith,
and
J.Min
(2009).
Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2.
|
| |
Nucleic Acids Res,
37,
2204-2210.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.Edwards
(2008).
Bermuda Principles meet structural biology.
|
| |
Nat Struct Mol Biol,
15,
116.
|
|
|
|
|
|
|
C.Xu,
G.Cui,
M.V.Botuyan,
and
G.Mer
(2008).
Structural basis for the recognition of methylated histone H3K36 by the Eaf3 subunit of histone deacetylase complex Rpd3S.
|
| |
Structure,
16,
1740-1750.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.K.Sims,
and
J.C.Rice
(2008).
PR-Set7 establishes a repressive trans-tail histone code that regulates differentiation.
|
| |
Mol Cell Biol,
28,
4459-4468.
|
|
|
|
|
|
|
M.Lange,
B.Kaynak,
U.B.Forster,
M.Tönjes,
J.J.Fischer,
C.Grimm,
J.Schlesinger,
S.Just,
I.Dunkel,
T.Krueger,
S.Mebus,
H.Lehrach,
R.Lurz,
J.Gobom,
W.Rottbauer,
S.Abdelilah-Seyfried,
and
S.Sperling
(2008).
Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex.
|
| |
Genes Dev,
22,
2370-2384.
|
|
|
|
|
|
|
M.S.Huen,
S.M.Sy,
J.M.van Deursen,
and
J.Chen
(2008).
Direct interaction between SET8 and proliferating cell nuclear antigen couples H4-K20 methylation with DNA replication.
|
| |
J Biol Chem,
283,
11073-11077.
|
|
|
|
|
|
|
N.Nady,
J.Min,
M.S.Kareta,
F.Chédin,
and
C.H.Arrowsmith
(2008).
A SPOT on the chromatin landscape? Histone peptide arrays as a tool for epigenetic research.
|
| |
Trends Biochem Sci,
33,
305-313.
|
|
|
|
|
|
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.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
|
Links
