2XDP - JenaLib

Title :   CRYSTAL STRUCTURE OF THE TUDOR DOMAIN OF HUMAN JMJD2C

Authors :   W. W. Yue, C. Gileadi, T. Krojer, H. Weisbach, E. Ugochukwu, M. Daniel, C. Phillips, A. Chaikuad, F. Von Delft, C. Allerston, C. Arrowsmith, J. Weigelt, A. Edwards, C. Bountra, U. Oppermann

Date :   06 May 10 (Deposition) - 09 Jun 10 (Release) - 05 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.56

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Oxidoreductase, Histone Modification (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. W. Yue, C. Gileadi, T. Krojer, H. Weisbach, E. Ugochukwu, M. Daniel, C. Phillips, A. Chaikuad, F. Von Delft, C. Allerston, C. Arrowsmith, J. Weigelt, A. Edwards, C. Bountra, U. Oppermann
Crystal Structure Of The Tudor Domain Of Human Jmjd2C
To Be Published
PubMed: search

Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 4C
	Chains	:	A
	EC Number	:	1.14.11.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3
	Expression System Vector	:	PNIC28-BSA4
	Fragment	:	TUDOR DOMAIN, RESIDUES 875-995
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	JMJD2C, JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3C, JUMONJI DOMAIN-CONTAINING PROTEIN 2C, GENE AMPLIFIED IN SQUAMOUS CELL CARCINOMA 1 PROTEIN, GASC-1 PROTEIN

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:119
 aligned with KDM4C_HUMAN | Q9H3R0 from UniProtKB/Swiss-Prot  Length:1056

    Alignment length:119
                                   885       895       905       915       925       935       945       955       965       975       985         
          KDM4C_HUMAN   876 EKVISVGQTVITKHRNTRYYSCRVMAVTSQTFYEVMFDDGSFSRDTFPEDIVSRDCLKLGPPAEGEVVQVKWPDGKLYGAKYFGSNIAHMYQVEFEDGSQIAMKREDIYTLDEELPKRV 994
               SCOP domains d2xdpa1 A:876-935 automated matches                         d2xdpa2 A:936-994 automated matches                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................eeeeeeeeeeeeeee....eeeeehhhh....hhhhhh......eeeee.....eeeeeeeeeeeeeeeeee.....eeeee.hhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2xdp A 876 EKVISVGQTVITKHRNTRYYSCRVMAVTSQTFYEVMFDDGSFSRDTFPEDIVSRDCLKLGPPAEGEVVQVKWPDGKLYGAKYFGSNIAHMYQVEFEDGSQIAMKREDIYTLDEELPKRV 994
                                   885       895       905       915       925       935       945       955       965       975       985

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (17, 17)

Asymmetric Unit(hide GO term definitions)

Chain A (KDM4C_HUMAN | Q9H3R0)

molecular function
	GO:0050681	androgen receptor binding	Interacting selectively and non-covalently with an androgen receptor.
	GO:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0032452	histone demethylase activity	Catalysis of the removal of a methyl group from a histone.
	GO:0032454	histone demethylase activity (H3-K9 specific)	Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0033169	histone H3-K9 demethylation	The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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