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PDBsum entry 2mny
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Oxidoreductase
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PDB id
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2mny
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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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Nmr structure of kdm5b phd1 finger
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Structure:
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Lysine-specific demethylase 5b. Chain: a. Fragment: zinc finger domain phd1, residues 306-360. Synonym: cancer/testis antigen 31, ct31, histone demethylase jarid1b, jumonji/arid domain-containing protein 1b, plu-1, retinoblastoma- binding protein 2 homolog 1, rbp2-h1. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: kdm5b. Expressed in: escherichia coli. Expression_system_taxid: 562.
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NMR struc:
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20 models
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Authors:
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Y.Zhang,H.R.Yang,X.Guo,N.Y.Rong,Y.J.Song,Y.W.Xu,W.X.Lan,Y.H.Xu,C.Cao
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Key ref:
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Y.Zhang
et al.
(2014).
The PHD1 finger of KDM5B recognizes unmodified H3K4 during the demethylation of histone H3K4me2/3 by KDM5B.
Protein Cell,
5,
837-850.
PubMed id:
DOI:
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Date:
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16-Apr-14
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Release date:
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06-Aug-14
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PROCHECK
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Headers
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References
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Q9UGL1
(KDM5B_HUMAN) -
Lysine-specific demethylase 5B from Homo sapiens
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Seq:
Struc:
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1544 a.a.
55 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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Enzyme class:
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E.C.1.14.11.67
- [histone H3]-trimethyl-L-lysine(4) demethylase.
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Reaction:
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N6,N6,N6-trimethyl-L-lysyl4-[histone H3] + 3 2-oxoglutarate + 3 O2 = L-lysyl4-[histone H3] + 3 formaldehyde + 3 succinate + 3 CO2
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N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3]
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+
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3
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2-oxoglutarate
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+
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3
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O2
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=
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L-lysyl(4)-[histone H3]
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+
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3
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formaldehyde
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+
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3
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succinate
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+
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3
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CO2
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Protein Cell
5:837-850
(2014)
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PubMed id:
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The PHD1 finger of KDM5B recognizes unmodified H3K4 during the demethylation of histone H3K4me2/3 by KDM5B.
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Y.Zhang,
H.Yang,
X.Guo,
N.Rong,
Y.Song,
Y.Xu,
W.Lan,
X.Zhang,
M.Liu,
Y.Xu,
C.Cao.
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ABSTRACT
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KDM5B is a histone H3K4me2/3 demethylase. The PHD1 domain of KDM5B is critical
for demethylation, but the mechanism underlying the action of this domain is
unclear. In this paper, we observed that PHD1KDM5B interacts with unmethylated
H3K4me0. Our NMR structure of PHD1KDM5B in complex with H3K4me0 revealed that
the binding mode is slightly different from that of other reported PHD fingers.
The disruption of this interaction by double mutations on the residues in the
interface (L325A/D328A) decreases the H3K4me2/3 demethylation activity of KDM5B
in cells by approximately 50% and increases the transcriptional repression of
tumor suppressor genes by approximately twofold. These findings imply that
PHD1KDM5B may help maintain KDM5B at target genes to mediate the demethylation
activities of KDM5B.
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Links
