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Title :   CRYSTAL STRUCTURE OF HUMAN JMJD2C CATALYTIC DOMAIN

Authors :   W. W. Yue, C. Gileadi, T. Krojer, A. C. W. Pike, F. Von Delft, S. Ng, L. Car C. Arrowsmith, J. Weigelt, A. Edwards, C. Bountra, U. Oppermann

Date :   28 Jul 10 (Deposition) - 29 Sep 10 (Release) - 13 May 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.55

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

Keywords :   Oxidoreductase, Transcription Regulation, Metal Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Hillringhaus, W. W. Yue, N. R. Rose, S. S. Ng, C. Gileadi, C. Loenarz, S. H. Bello, J. E. Bray, C. J. Schofield, U. Oppermann
Structural And Evolutionary Basis For The Dual Substrate Selectivity Of Human Kdm4 Histone Demethylase Family.
J. Biol. Chem. V. 286 41616 2011
PubMed-ID: 21914792 | Reference-DOI: 10.1074/JBC.M111.283689

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 4C
	Chains	:	A, B
	EC Number	:	1.14.11.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3-PRARE2
	Expression System Vector	:	PNIC28-BSA4
	Fragment	:	JUMONJI DOMAIN, RESIDUES 1-347
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3C, JMJD2C, GENE AMPLIFIED IN SQUAMOUS CELL CARCINOMA 1 PROTEIN, GASC-1 PROTEIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 10)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
3	NI	2	Ligand/Ion	NICKEL (II) ION
4	OGA	2	Ligand/Ion	N-OXALYLGLYCINE
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
3	NI	-1	Ligand/Ion	NICKEL (II) ION
4	OGA	1	Ligand/Ion	N-OXALYLGLYCINE
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	NI	-1	Ligand/Ion	NICKEL (II) ION
4	OGA	1	Ligand/Ion	N-OXALYLGLYCINE
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:134 , PHE A:187 , HIS A:190 , GLU A:192 , SER A:198 , ASN A:200 , LYS A:208 , HIS A:278 , NI A:1348	BINDING SITE FOR RESIDUE OGA A 601
02	AC2	SOFTWARE	TYR B:134 , PHE B:187 , HIS B:190 , GLU B:192 , SER B:198 , ASN B:200 , LYS B:208 , TRP B:210 , HIS B:278 , NI B:1348 , HOH B:2072 , HOH B:2145	BINDING SITE FOR RESIDUE OGA B 601
03	AC3	SOFTWARE	HIS A:190 , GLU A:192 , HIS A:278 , OGA A:601 , HOH A:2084	BINDING SITE FOR RESIDUE NI A1348
04	AC4	SOFTWARE	HIS B:190 , GLU B:192 , HIS B:278 , OGA B:601 , HOH B:2072	BINDING SITE FOR RESIDUE NI B1348
05	AC5	SOFTWARE	CYS A:236 , HIS A:242 , CYS A:308 , CYS A:310	BINDING SITE FOR RESIDUE ZN A1349
06	AC6	SOFTWARE	CYS B:236 , HIS B:242 , CYS B:308 , CYS B:310	BINDING SITE FOR RESIDUE ZN B1349
07	AC7	SOFTWARE	PHE A:204 , GLY A:205 , ALA A:266 , LYS A:335 , HOH A:2090	BINDING SITE FOR RESIDUE EDO A1350
08	AC8	SOFTWARE	ALA A:266 , GLY A:267 , GLU A:268	BINDING SITE FOR RESIDUE EDO A1351
09	AC9	SOFTWARE	ASP A:115 , TYR A:116 , ARG A:324	BINDING SITE FOR RESIDUE EDO A1352
10	BC1	SOFTWARE	ASN A:126 , TRP A:183 , HOH A:2079 , ARG B:112	BINDING SITE FOR RESIDUE CL A1353

(no "SS Bond" information available for 2XML)

(no "Cis Peptide Bond" information available for 2XML)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049660	E	206	D	KDM4C_HUMAN	Polymorphism	7864351	A/B	E	206	D

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049660	E	206	D	KDM4C_HUMAN	Polymorphism	7864351	A	E	206	D

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049660	E	206	D	KDM4C_HUMAN	Polymorphism	7864351	B	E	206	D

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJN	PS51183	JmjN domain profile.	KDM4C_HUMAN	16-58	2	A:16-58 B:16-58
2	JMJC	PS51184	JmjC domain profile.	KDM4C_HUMAN	144-310	2	A:144-310 B:144-310

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJN	PS51183	JmjN domain profile.	KDM4C_HUMAN	16-58	1	A:16-58 -
2	JMJC	PS51184	JmjC domain profile.	KDM4C_HUMAN	144-310	1	A:144-310 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJN	PS51183	JmjN domain profile.	KDM4C_HUMAN	16-58	1	- B:16-58
2	JMJC	PS51184	JmjC domain profile.	KDM4C_HUMAN	144-310	1	- B:144-310

(no "Exon" information available for 2XML)

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)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:338
 aligned with KDM4C_HUMAN | Q9H3R0 from UniProtKB/Swiss-Prot  Length:1056

    Alignment length:338
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339        
          KDM4C_HUMAN    10 LNPSCKIMTFRPSMEEFREFNKYLAYMESKGAHRAGLAKVIPPKEWKPRQCYDDIDNLLIPAPIQQMVTGQSGLFTQYNIQKKAMTVKEFRQLANSGKYCTPRYLDYEDLERKYWKNLTFVAPIYGADINGSIYDEGVDEWNIARLNTVLDVVEEECGISIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAQGFFPSSSQGCDAFLRHKMTLISPSVLKKYGIPFDKITQEAGEFMITFPYGYHAGFNHGFNCAESTNFATVRWIDYGKVAKLCTCRKDMVKISMDIFVRKFQPDRYQLWKQGKDIYTIDHTK 347
               SCOP domains d2xmla_ A: automated matches                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee...........hhhhhh.ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee.hhhhhhhhh...............hhhhhhhhh..hhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------JMJN  PDB: A:16-58 UniProt: 16-58          -------------------------------------------------------------------------------------JMJC  PDB: A:144-310 UniProt: 144-310                                                                                                                                  ------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xml A  10 LNPSCKIMTFRPSMEEFREFNKYLAYMESKGAHRAGLAKVIPPKEWKPRQCYDDIDNLLIPAPIQQMVTGQSGLFTQYNIQKKAMTVKEFRQLANSGKYCTPRYLDYEDLERKYWKNLTFVAPIYGADINGSIYDEGVDEWNIARLNTVLDVVEEECGISIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAQGFFPSSSQGCDAFLRHKMTLISPSVLKKYGIPFDKITQEAGEFMITFPYGYHAGFNHGFNCAESTNFATVRWIDYGKVAKLCTCRKDMVKISMDIFVRKFQPDRYQLWKQGKDIYTIDHTK 347
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339

Chain B from PDB  Type:PROTEIN  Length:338
 aligned with KDM4C_HUMAN | Q9H3R0 from UniProtKB/Swiss-Prot  Length:1056

    Alignment length:338
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339        
          KDM4C_HUMAN    10 LNPSCKIMTFRPSMEEFREFNKYLAYMESKGAHRAGLAKVIPPKEWKPRQCYDDIDNLLIPAPIQQMVTGQSGLFTQYNIQKKAMTVKEFRQLANSGKYCTPRYLDYEDLERKYWKNLTFVAPIYGADINGSIYDEGVDEWNIARLNTVLDVVEEECGISIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAQGFFPSSSQGCDAFLRHKMTLISPSVLKKYGIPFDKITQEAGEFMITFPYGYHAGFNHGFNCAESTNFATVRWIDYGKVAKLCTCRKDMVKISMDIFVRKFQPDRYQLWKQGKDIYTIDHTK 347
               SCOP domains d2xmlb_ B: automated matches                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------JmjN-2xmlB03 B:17-51               -----------------------------------------------------------------------------------------------------------------------------JmjC-2xmlB01 B:177-293                                                                                               ------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -------JmjN-2xmlB04 B:17-51               -----------------------------------------------------------------------------------------------------------------------------JmjC-2xmlB02 B:177-293                                                                                               ------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .......eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee...........hhhhhh.ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee.hhhhhhhhh...............hhhhhhhhh..hhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------JMJN  PDB: B:16-58 UniProt: 16-58          -------------------------------------------------------------------------------------JMJC  PDB: B:144-310 UniProt: 144-310                                                                                                                                  ------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xml B  10 LNPSCKIMTFRPSMEEFREFNKYLAYMESKGAHRAGLAKVIPPKEWKPRQCYDDIDNLLIPAPIQQMVTGQSGLFTQYNIQKKAMTVKEFRQLANSGKYCTPRYLDYEDLERKYWKNLTFVAPIYGADINGSIYDEGVDEWNIARLNTVLDVVEEECGISIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAQGFFPSSSQGCDAFLRHKMTLISPSVLKKYGIPFDKITQEAGEFMITFPYGYHAGFNHGFNCAESTNFATVRWIDYGKVAKLCTCRKDMVKISMDIFVRKFQPDRYQLWKQGKDIYTIDHTK 347
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: Clavaminate synthase-like (197)

Family: Histone demethylase core (19)

Protein domain: automated matches (3)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d2xmla_	A:
1b	d2xmlb_	B:

(no "CATH Domain" information available for 2XML)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cupin (179)

Family: JmjC (39)

Homo sapiens (Human) (31)

1a	JmjC-2xmlB01	B:177-293
1b	JmjC-2xmlB02	B:177-293

Clan: no clan defined [family: JmjN] (16)

Family: JmjN (16)

Homo sapiens (Human) (16)

2a	JmjN-2xmlB03	B:17-51
2b	JmjN-2xmlB04	B:17-51

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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2xdp	CRYSTAL STRUCTURE OF THE TUDOR DOMAIN OF HUMAN JMJD2C

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