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PDBsum entry 3n9l
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Oxidoreductase
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PDB id
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3n9l
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Oxidoreductase
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Title:
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Cekdm7a from c.Elegans, complex with h3k4me3 peptide and nog
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Structure:
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Putative uncharacterized protein. Chain: a. Fragment: phd domain, unp residues 201-724. Synonym: lysine demethylase. Engineered: yes. Histone h3 peptide. Chain: b. Fragment: jmjc domain, unp residues 2-16. Engineered: yes.
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Source:
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Caenorhabditis elegans. Organism_taxid: 6239. Gene: f29b9.2. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Other_details: chemical synthesis, purchased from a company
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Resolution:
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2.80Å
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R-factor:
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0.200
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R-free:
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0.255
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Authors:
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Y.Yang,L.Hu,P.Wang,H.Hou,C.D.Chen,Y.Xu
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Key ref:
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Y.Yang
et al.
(2010).
Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans.
Cell Res,
20,
886-898.
PubMed id:
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Date:
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31-May-10
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Release date:
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30-Jun-10
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PROCHECK
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Headers
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References
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Q9GYI0
(KDM7_CAEEL) -
Lysine-specific demethylase 7 homolog from Caenorhabditis elegans
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Seq:
Struc:
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910 a.a.
486 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Cell Res
20:886-898
(2010)
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PubMed id:
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Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans.
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Y.Yang,
L.Hu,
P.Wang,
H.Hou,
Y.Lin,
Y.Liu,
Z.Li,
R.Gong,
X.Feng,
L.Zhou,
W.Zhang,
Y.Dong,
H.Yang,
H.Lin,
Y.Wang,
C.D.Chen,
Y.Xu.
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ABSTRACT
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Histone lysine methylation can be removed by JmjC domain-containing proteins in
a sequence- and methylation-state-specific manner. However, how substrate
specificity is determined and how the enzymes are regulated were largely
unknown. We recently found that ceKDM7A, a PHD- and JmjC domain-containing
protein, is a histone demethylase specific for H3K9me2 and H3K27me2, and the PHD
finger binding to H3K4me3 guides the demethylation activity in vivo. To provide
structural insight into the molecular mechanisms for the enzymatic activity and
the function of the PHD finger, we solved six crystal structures of the enzyme
in apo form and in complex with single or two peptides containing various
combinations of H3K4me3, H3K9me2, and H3K27me2 modifications. The structures
indicate that H3K9me2 and H3K27me2 interact with ceKDM7A in a similar fashion,
and that the peptide-binding specificity is determined by a network of specific
interactions. The geometrical measurement of the structures also revealed that
H3K4me3 associated with the PHD finger and H3K9me2 bound to the JmjC domain are
from two separate molecules, suggesting a trans-histone peptide-binding
mechanism. Thus, our systemic structural studies reveal not only the substrate
recognition by the catalytic domain but also more importantly, the molecular
mechanism of dual specificity of ceDKM7A for both H3K9me2 and H3K27me2.Cell
Research advance online publication 22 June 2010; doi: 10.1038/cr.2010.86.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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L.Kruidenier,
C.W.Chung,
Z.Cheng,
J.Liddle,
K.Che,
G.Joberty,
M.Bantscheff,
C.Bountra,
A.Bridges,
H.Diallo,
D.Eberhard,
S.Hutchinson,
E.Jones,
R.Katso,
M.Leveridge,
P.K.Mander,
J.Mosley,
C.Ramirez-Molina,
P.Rowland,
C.J.Schofield,
R.J.Sheppard,
J.E.Smith,
C.Swales,
R.Tanner,
P.Thomas,
A.Tumber,
G.Drewes,
U.Oppermann,
D.J.Patel,
K.Lee,
and
D.M.Wilson
(2012).
A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response.
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Nature,
488,
404-408.
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PDB codes:
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S.Krishnan,
S.Horowitz,
and
R.C.Trievel
(2011).
Structure and function of histone H3 lysine 9 methyltransferases and demethylases.
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Chembiochem,
12,
254-263.
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H.Lin,
Y.Wang,
Y.Wang,
F.Tian,
P.Pu,
Y.Yu,
H.Mao,
Y.Yang,
P.Wang,
L.Hu,
Y.Lin,
Y.Liu,
Y.Xu,
and
C.D.Chen
(2010).
Coordinated regulation of active and repressive histone methylations by a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans.
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Cell Res,
20,
899-907.
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T.Suganuma,
and
J.L.Workman
(2010).
Features of the PHF8/KIAA1718 histone demethylase.
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Cell Res,
20,
861-862.
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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.
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Links
