3N9M - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CEKDM7A FROM C.ELEGANS, ALONE

Authors :   Y. Yang, L. Hu, P. Wang, H. Hou, C. D. Chen, Y. Xu

Date :   31 May 10 (Deposition) - 30 Jun 10 (Release) - 11 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.49

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

Keywords :   Histone, Methylation, Demethylase, Phd, Jmjc, Fe(Ii) And Alpha-Kg (Alpha-Ketoglutarate)-Dependent Dioxygenase Family, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   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
Structural Insights Into A Dual-Specificity Histone Demethylase Cekdm7A From Caenorhabditis Elegans
Cell Res. V. 20 886 2010
PubMed-ID: 20567261 | Reference-DOI: 10.1038/CR.2010.86

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
	Chains	:	A, C
	EC Number	:	1.14.11.27
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	PHD DOMAIN, UNP RESIDUES 201-724
	Gene	:	F29B9.2
	Organism Scientific	:	CAENORHABDITIS ELEGANS
	Organism Taxid	:	6239
	Synonym	:	LYSINE DEMETHYLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	FE2	2	Ligand/Ion	FE (II) ION
2	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	FE2	1	Ligand/Ion	FE (II) ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	FE2	1	Ligand/Ion	FE (II) ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:53 , HIS A:495 , ASP A:497 , HIS A:567	BINDING SITE FOR RESIDUE FE2 A 1
2	AC2	SOFTWARE	CYS A:198 , CYS A:201 , HIS A:252 , CYS A:255	BINDING SITE FOR RESIDUE ZN A 2
3	AC3	SOFTWARE	CYS A:244 , CYS A:247 , CYS A:271 , CYS A:274	BINDING SITE FOR RESIDUE ZN A 3
4	AC4	SOFTWARE	HOH C:23 , HIS C:495 , ASP C:497 , HIS C:567	BINDING SITE FOR RESIDUE FE2 C 1
5	AC5	SOFTWARE	CYS C:198 , CYS C:201 , HIS C:252 , CYS C:255	BINDING SITE FOR RESIDUE ZN C 2
6	AC6	SOFTWARE	CYS C:244 , CYS C:247 , CYS C:271 , CYS C:274	BINDING SITE FOR RESIDUE ZN C 3

(no "SS Bond" information available for 3N9M)

Asymmetric Unit

No.	Residues
1	His A:206	-	Glu A:207
2	Tyr C:470	-	Leu C:471

(no "SAP(SNP)/Variant" information available for 3N9M)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	KDM7_CAEEL	211-287	2	A:198-274 C:198-274
2	JMJC	PS51184	JmjC domain profile.	KDM7_CAEEL	441-612	2	A:428-599 C:428-599

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	KDM7_CAEEL	211-287	1	A:198-274 -
2	JMJC	PS51184	JmjC domain profile.	KDM7_CAEEL	441-612	1	A:428-599 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	KDM7_CAEEL	211-287	1	- C:198-274
2	JMJC	PS51184	JmjC domain profile.	KDM7_CAEEL	441-612	1	- C:428-599

(no "Exon" information available for 3N9M)

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:503
 aligned with KDM7_CAEEL | Q9GYI0 from UniProtKB/Swiss-Prot  Length:910

    Alignment length:514
                                   215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715    
           KDM7_CAEEL   206 KESDRCGGCGKFTHEDDLIALEEEKKKEKEKPLMSKKKSHHHKKNDFQWIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPHTGHSIRYKVVAPHRYRWYSPNEKHLGIEVGSKTWIEDFITRENTVPSPTDDEVCIVEDGYEFRREFEKLGGADNWGKVFMVKDMDGLNMTMPKPGFDLEDVVKIMGSDYEVDTIDVYNQSTYSMKLDTFRKLFRDTKNRPLLYNFLSLEFSDNNEMKEIAKPPRFVQEISMVNRLWPDVSGAEYIKLLQREEYLPEDQRPKVEQFCLAGMAGSYTDFHVDFGGSSVYYHILKGEKIFYIAAPTEQNFAAYQAHETSPDTTTWFGDIANGAVKRVVIKEGQTLLIPAGWIHAVLTPVDSLVFGGNFLHLGNLEMQMRVYHLENAIRKEIRSEEKFYFPNFELLHWMYMRNVLLEKITEANQEGSDMREQEKNIWTASQIMKAEMERWMDRELRLGPEKNAILPTDDKNKIMISVRKQIEIQTKIQNAKNK 719
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................-----------..........hhhhh.eeeee......eeee.hhh.hhhhh..eee.....hhhhhh..ee............hhhhh.......hhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhh......eee.hhheee..hhhhhhhhhhh.......eee.........hhhhhh..hhhhhh.hhhhhhh....hhhhhhhh......hhhhh.....eeeee...eeeeee.hhhhheeeeeeeeeeeeeeee..hhhhhhhhhhhhhh.....hhhhhh....eeeee....eeee....eeeeeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----ZF_PHD_1  PDB: A:198-274 UniProt: 211-287                                    ---------------------------------------------------------------------------------------------------------------------------------------------------------JMJC  PDB: A:428-599 UniProt: 441-612                                                                                                                                       ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n9m A 193 KESDRCGGCGKFTHEDDLI-----------KPLMSKKKSHHHKKNDFQWIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPHTGHSIRYKVVAPHRYRWYSPNEKHLGIEVGSKTWIEDFITRENTVPSPTDDEVCIVEDGYEFRREFEKLGGADNWGKVFMVKDMDGLNMTMPKPGFDLEDVVKIMGSDYEVDTIDVYNQSTYSMKLDTFRKLFRDTKNRPLLYNFLSLEFSDNNEMKEIAKPPRFVQEISMVNRLWPDVSGAEYIKLLQREEYLPEDQRPKVEQFCLAGMAGSYTDFHVDFGGSSVYYHILKGEKIFYIAAPTEQNFAAYQAHETSPDTTTWFGDIANGAVKRVVIKEGQTLLIPAGWIHAVLTPVDSLVFGGNFLHLGNLEMQMRVYHLENAIRKEIRSEEKFYFPNFELLHWMYMRNVLLEKITEANQEGSDMREQEKNIWTASQIMKAEMERWMDRELRLGPEKNAILPTDDKNKIMISVRKQIEIQTKIQNAKNK 706
                                   202        |-         -|      232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702    
                                            211         223

Chain C from PDB  Type:PROTEIN  Length:481
 aligned with KDM7_CAEEL | Q9GYI0 from UniProtKB/Swiss-Prot  Length:910

    Alignment length:514
                                   215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715    
           KDM7_CAEEL   206 KESDRCGGCGKFTHEDDLIALEEEKKKEKEKPLMSKKKSHHHKKNDFQWIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPHTGHSIRYKVVAPHRYRWYSPNEKHLGIEVGSKTWIEDFITRENTVPSPTDDEVCIVEDGYEFRREFEKLGGADNWGKVFMVKDMDGLNMTMPKPGFDLEDVVKIMGSDYEVDTIDVYNQSTYSMKLDTFRKLFRDTKNRPLLYNFLSLEFSDNNEMKEIAKPPRFVQEISMVNRLWPDVSGAEYIKLLQREEYLPEDQRPKVEQFCLAGMAGSYTDFHVDFGGSSVYYHILKGEKIFYIAAPTEQNFAAYQAHETSPDTTTWFGDIANGAVKRVVIKEGQTLLIPAGWIHAVLTPVDSLVFGGNFLHLGNLEMQMRVYHLENAIRKEIRSEEKFYFPNFELLHWMYMRNVLLEKITEANQEGSDMREQEKNIWTASQIMKAEMERWMDRELRLGPEKNAILPTDDKNKIMISVRKQIEIQTKIQNAKNK 719
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------JmjC-3n9mC01 C:482-582                                                                               ---------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------JmjC-3n9mC02 C:482-582                                                                               ---------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...............------------------....hhhhhh...eeeee......eeee.....hhhhh..eee.....hhhhhh..ee............hhhhh.......hhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhh...eeeeee....eeeeeehhhhhhhhhh.......eee.........hhhhhh..hhhhhhhhhhhhhh.---------------..hhhhh.....eeeee...eeeeeee.hhhheeeeeeeeeeeeeeee..hhhhhhhhhhhhhh.....hhhhhh....eeeee....eeee....eeeeeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----ZF_PHD_1  PDB: C:198-274 UniProt: 211-287                                    ---------------------------------------------------------------------------------------------------------------------------------------------------------JMJC  PDB: C:428-599 UniProt: 441-612                                                                                                                                       ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n9m C 193 KESDRCGGCGKFTHE------------------MSKKKSHHHKKNDFQWIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPHTGHSIRYKVVAPHRYRWYSPNEKHLGIEVGSKTWIEDFITRENTVPSPTDDEVCIVEDGYEFRREFEKLGGADNWGKVFMVKDMDGLNMTMPKPGFDLEDVVKIMGSDYEVDTIDVYNQSTYSMKLDTFRKLFRDTKNRPLLYNFLSLEFSDNNEMKEIAKPPRFVQEISMVNRLWP---------------YLPEDQRPKVEQFCLAGMAGSYTDFHVDFGGSSVYYHILKGEKIFYIAAPTEQNFAAYQAHETSPDTTTWFGDIANGAVKRVVIKEGQTLLIPAGWIHAVLTPVDSLVFGGNFLHLGNLEMQMRVYHLENAIRKEIRSEEKFYFPNFELLHWMYMRNVLLEKITEANQEGSDMREQEKNIWTASQIMKAEMERWMDRELRLGPEKNAILPTDDKNKIMISVRKQIEIQTKIQNAKNK 706
                                   202    |    -         -   |   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452 |       -       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702    
                                        207                226                                                                                                                                                                                                                                 454             470

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 '\|'

(no "SCOP Domain" information available for 3N9M)

(no "CATH Domain" information available for 3N9M)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cupin (179)

Family: JmjC (39)

Caenorhabditis elegans (8)

1a	JmjC-3n9mC01	C:482-582
1b	JmjC-3n9mC02	C:482-582

Asymmetric Unit(hide GO term definitions)

Chain A,C (KDM7_CAEEL | Q9GYI0)

molecular function
	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:0042393	histone binding	Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
	GO:0071558	histone demethylase activity (H3-K27 specific)	Catalysis of the removal of a methyl group from lysine at position 27 of the histone H3 protein.
	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:0071557	histone H3-K27 demethylation	The modification of histone H3 by the removal of a methyl group from lysine at position 27 of the histone.
	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:0040012	regulation of locomotion	Any process that modulates the frequency, rate or extent of locomotion of a cell or organism.
	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: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.

Asymmetric Unit
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	Cis Peptide Bonds
		His A:206 - Glu A:207	[ RasMol ]
		Tyr C:470 - Leu C:471	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3n9m
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	1.14.11.27
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UniProtKB/Swiss-Prot
	KDM7_CAEEL \| Q9GYI0	:	3n9l 3n9n 3n9o 3n9p 3n9q 3puq 3pur

3n9l	LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3) AND NOG
3n9n	LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3K9ME2) AND NOG
3n9o	LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3) AND HISTONE H3(K9ME2) AND NOG
3n9p	LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3K27ME2) AND NOG
3n9q	LYSINE DEMETHYLASE WITH HISTONE H3(K4ME3) AND HISTONE H3(K27ME2) AND NOG

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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SCOP Domains (0, 0)

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Pfam Domains (1, 2)

Gene Ontology (14, 14)

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