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PDBsum entry 4o64
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Metal binding protein
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PDB id
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4o64
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PDB id:
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Metal binding protein
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Title:
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Zinc fingers of kdm2b
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Structure:
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Lysine-specific demethylase 2b. Chain: a, b, c. Fragment: unp residues 607-723. Synonym: cxxc-type zinc finger protein 2, f-box and leucine-rich repeat protein 10, f-box protein fbl10, f-box/lrr-repeat protein 10, jmjc domain-containing histone demethylation protein 1b, jumonji domain-containing emsy-interactor methyltransferase motif protein, protein jemma, protein-containing cxxc domain 2, [histone-h3]-lysine- 36 demethylase 1b.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: kdm2b, cxxc2, fbl10, fbxl10, jhdm1b, pccx2. Expressed in: escherichia coli. Expression_system_taxid: 469008.
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Resolution:
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2.13Å
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R-factor:
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0.191
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R-free:
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0.220
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Authors:
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K.Liu,C.Xu,W.Tempel,J.R.Walker,C.H.Arrowsmith,C.Bountra,A.M.Edwards, J.Min,Structural Genomics Consortium (Sgc)
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Key ref:
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C.Xu
et al.
(2018).
DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.
Structure,
26,
85.
PubMed id:
DOI:
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Date:
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20-Dec-13
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Release date:
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16-Apr-14
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PROCHECK
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Headers
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References
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Q8NHM5
(KDM2B_HUMAN) -
Lysine-specific demethylase 2B from Homo sapiens
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Seq:
Struc:
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1336 a.a.
116 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.1.14.11.27
- [histone H3]-dimethyl-L-lysine(36) demethylase.
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Reaction:
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N6,N6-dimethyl-L-lysyl36-[histone H3] + 2 2-oxoglutarate + 2 O2 = L-lysyl36-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2
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N(6),N(6)-dimethyl-L-lysyl(36)-[histone H3]
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+
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2
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2-oxoglutarate
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+
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2
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O2
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=
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L-lysyl(36)-[histone H3]
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+
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2
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formaldehyde
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+
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2
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succinate
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+
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2
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CO2
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Cofactor:
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Fe(2+)
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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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Structure
26:85
(2018)
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PubMed id:
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DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.
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C.Xu,
K.Liu,
M.Lei,
A.Yang,
Y.Li,
T.R.Hughes,
J.Min.
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ABSTRACT
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The CXXC domain, first identified as the reader of unmodified CpG dinucleotide,
plays important roles in epigenetic regulation by targeting various activities
to CpG islands. Here we systematically measured and compared the DNA-binding
selectivities of all known human CXXC domains by different binding assays, and
complemented the existing function-based classification of human CXXC domains
with a classification based on their DNA selectivities. Through a series of
crystal structures of CXXC domains with DNA ligands, we unravel the molecular
mechanisms of how these CXXC domains, including single CXXC domains and tandem
CXXC-PHD domains, recognize distinct DNA ligands, which further supports our
classification of human CXXC domains and also provides insights into selective
recruitment of chromatin modifiers to their respective targets via CXXC domains
recognizing different genomic DNA sequences. Our study facilitates
the understanding of the relationship between the DNA-binding specificities of
the CXXC proteins and their biological functions.
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Links
