3PUR - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CEKDM7A FROM C.ELEGANS, COMPLEX WITH D-2-HG

Authors :   Y. Yang, P. Wang, W. Xu, Y. Xu

Date :   06 Dec 10 (Deposition) - 26 Jan 11 (Release) - 28 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Demethylase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Xu, H. Yang, Y. Liu, Y. Yang, P. Wang, S. -H. Kim, S. Ito, C. Yang, P. Wang, M. -T. Xiao, L. -X. Liu, W. -Q. Jiang, J. Liu, J. -Y. Zhang, B. Wang, S. Frye, Y. Zhang, Y. -H. Xu, Q. -Y. Lei, K. -L. Guan, S. -M. Zhao, Y. Xiong
Oncometabolite 2-Hydroxyglutarate Is A Competitive Inhibito Of Alpha-Ketoglutarate-Dependent Dioxygenases
Cancer Cell V. 19 17 2011
PubMed-ID: 21251613 | Reference-DOI: 10.1016/J.CCR.2010.12.014

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 7 HOMOLOG
	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	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PHD DOMAIN
	Gene	:	F29B9.2
	Organism Common	:	NEMATODE
	Organism Scientific	:	CAENORHABDITIS ELEGANS
	Organism Taxid	:	6239
	Synonym	:	LYSINE DEMETHYLASE, CEKDM7A, PHD FINGER PROTEIN 8 HOMOLOG, PHF8 HOMOLOG

		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 (3, 8)

No.	Name	Count	Type	Full Name
1	2HG	2	Ligand/Ion	(2R)-2-HYDROXYPENTANEDIOIC ACID
2	FE2	2	Ligand/Ion	FE (II) ION
3	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 2)

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

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:495 , ASP A:497 , HIS A:567 , 2HG A:1000 , HOH A:1065	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	FE2 A:1 , ASN A:421 , THR A:492 , HIS A:495 , ASP A:497 , TYR A:505 , LYS A:512 , HIS A:567 , VAL A:569 , HOH A:1031 , HOH A:1032 , HOH A:1065 , HOH A:1072 , HOH A:1279	BINDING SITE FOR RESIDUE 2HG A 1000
5	AC5	SOFTWARE	HIS C:495 , ASP C:497 , HIS C:567 , 2HG C:1000 , HOH C:1041	BINDING SITE FOR RESIDUE FE2 C 1
6	AC6	SOFTWARE	CYS C:198 , CYS C:201 , HIS C:252 , CYS C:255	BINDING SITE FOR RESIDUE ZN C 2
7	AC7	SOFTWARE	CYS C:244 , CYS C:247 , CYS C:271 , CYS C:274	BINDING SITE FOR RESIDUE ZN C 3
8	AC8	SOFTWARE	FE2 C:1 , THR C:492 , HIS C:495 , ASP C:497 , TYR C:505 , LYS C:512 , HIS C:567 , VAL C:569 , HOH C:1024 , HOH C:1041 , HOH C:1280 , HOH C:1282	BINDING SITE FOR RESIDUE 2HG C 1000

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

(no "Cis Peptide Bond" information available for 3PUR)

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

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 3PUR)

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:483
 aligned with KDM7_CAEEL | Q9GYI0 from UniProtKB/Swiss-Prot  Length:910

    Alignment length:515
                                   214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714     
           KDM7_CAEEL   205 PKESDRCGGCGKFTHEDDLIALEEEKKKEKEKPLMSKKKSHHHKKNDFQWIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPHTGHSIRYKVVAPHRYRWYSPNEKHLGIEVGSKTWIEDFITRENTVPSPTDDEVCIVEDGYEFRREFEKLGGADNWGKVFMVKDMDGLNMTMPKPGFDLEDVVKIMGSDYEVDTIDVYNQSTYSMKLDTFRKLFRDTKNRPLLYNFLSLEFSDNNEMKEIAKPPRFVQEISMVNRLWPDVSGAEYIKLLQREEYLPEDQRPKVEQFCLAGMAGSYTDFHVDFGGSSVYYHILKGEKIFYIAAPTEQNFAAYQAHETSPDTTTWFGDIANGAVKRVVIKEGQTLLIPAGWIHAVLTPVDSLVFGGNFLHLGNLEMQMRVYHLENAIRKEIRSEEKFYFPNFELLHWMYMRNVLLEKITEANQEGSDMREQEKNIWTASQIMKAEMERWMDRELRLGPEKNAILPTDDKNKIMISVRKQIEIQTKIQNAKNK 719
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............-------------------................eee......eee.hhh..hhhhh..eee.....hhhhhh..ee............hhhhh.......hhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhh...eeeeee....eeeeeehhhhhhhhhh.......eee..ee.....hhhhhh..hhhhhhhhhhhhhh...-------------..hhhhh.....eeeee...eeeeee.hhhhheeeeeeeeeeeeeeee..hhhhhhhhhhhhhh.....hhhhhh....eeeeee...eeee....eeeeeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh... 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
                 3pur A 192 PKESDRCGGCGKFT-------------------LMSKKKSHHHKKNDFQWIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPHTGHSIRYKVVAPHRYRWYSPNEKHLGIEVGSKTWIEDFITRENTVPSPTDDEVCIVEDGYEFRREFEKLGGADNWGKVFMVKDMDGLNMTMPKPGFDLEDVVKIMGSDYEVDTIDVYNQSTYSMKLDTFRKLFRDTKNRPLLYNFLSLEFSDNNEMKEIAKPPRFVQEISMVNRLWPDV-------------YLPEDQRPKVEQFCLAGMAGSYTDFHVDFGGSSVYYHILKGEKIFYIAAPTEQNFAAYQAHETSPDTTTWFGDIANGAVKRVVIKEGQTLLIPAGWIHAVLTPVDSLVFGGNFLHLGNLEMQMRVYHLENAIRKEIRSEEKFYFPNFELLHWMYMRNVLLEKITEANQEGSDMREQEKNIWTASQIMKAEMERWMDRELRLGPEKNAILPTDDKNKIMISVRKQIEIQTKIQNAKNK 706
                                   201   |     -         -   |   231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451    |    -       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701     
                                       205                 225                                                                                                                                                                                                                                    456           470

Chain C from PDB  Type:PROTEIN  Length:496
 aligned with KDM7_CAEEL | Q9GYI0 from UniProtKB/Swiss-Prot  Length:910

    Alignment length:515
                                   214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714     
           KDM7_CAEEL   205 PKESDRCGGCGKFTHEDDLIALEEEKKKEKEKPLMSKKKSHHHKKNDFQWIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPHTGHSIRYKVVAPHRYRWYSPNEKHLGIEVGSKTWIEDFITRENTVPSPTDDEVCIVEDGYEFRREFEKLGGADNWGKVFMVKDMDGLNMTMPKPGFDLEDVVKIMGSDYEVDTIDVYNQSTYSMKLDTFRKLFRDTKNRPLLYNFLSLEFSDNNEMKEIAKPPRFVQEISMVNRLWPDVSGAEYIKLLQREEYLPEDQRPKVEQFCLAGMAGSYTDFHVDFGGSSVYYHILKGEKIFYIAAPTEQNFAAYQAHETSPDTTTWFGDIANGAVKRVVIKEGQTLLIPAGWIHAVLTPVDSLVFGGNFLHLGNLEMQMRVYHLENAIRKEIRSEEKFYFPNFELLHWMYMRNVLLEKITEANQEGSDMREQEKNIWTASQIMKAEMERWMDRELRLGPEKNAILPTDDKNKIMISVRKQIEIQTKIQNAKNK 719
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------JmjC-3purC01 C:482-582                                                                               ---------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------JmjC-3purC02 C:482-582                                                                               ---------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...............------------------.....hhhhhh.....eee......eee.hhh..hhhhh..eee.....hhhhhh..ee............hhhhh.......hhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhh..eeeeee.............hhhhhhhhhh...eeeeee.hhheeeeeehhhhhhhhhh.......eee..ee.....hhhhhh..hhhhhhhhhhhhhh.....-hhhhhhh.....hhhhh.....eeeee...eeeeee.hhhhheeeeeeeeeeeeeeee..hhhhhhhhhhhhhh.....hhhhhh....eeeeee...eeee....eeeeeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh... 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
                 3pur C 192 PKESDRCGGCGKFTH------------------LMSKKKSHHHKKNDFQWIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPHTGHSIRYKVVAPHRYRWYSPNEKHLGIEVGSKTWIEDFITRENTVPSPTDDEVCIVEDGYEFRREFEKLGGADNWGKVFMVKDMDGLNMTMPKPGFDLEDVVKIMGSDYEVDTIDVYNQSTYSMKLDTFRKLFRDTKNRPLLYNFLSLEFSDNNEMKEIAKPPRFVQEISMVNRLWPDVSG-EYIKLLQREEYLPEDQRPKVEQFCLAGMAGSYTDFHVDFGGSSVYYHILKGEKIFYIAAPTEQNFAAYQAHETSPDTTTWFGDIANGAVKRVVIKEGQTLLIPAGWIHAVLTPVDSLVFGGNFLHLGNLEMQMRVYHLENAIRKEIRSEEKFYFPNFELLHWMYMRNVLLEKITEANQEGSDMREQEKNIWTASQIMKAEMERWMDRELRLGPEKNAILPTDDKNKIMISVRKQIEIQTKIQNAKNK 706
                                   201    |    -         -   |   231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451      |461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701     
                                        206                225                                                                                                                                                                                                                                      458 |                                                                                                                                                                                                                                                      
                                                                                                                                                                                                                                                                                                      460

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 3PUR)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cupin (179)

Family: JmjC (39)

Caenorhabditis elegans (8)

1a	JmjC-3purC01	C:482-582
1b	JmjC-3purC02	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.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3pur)

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	3pur
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	1.14.11.27
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	KDM7_CAEEL \| Q9GYI0	:	3n9l 3n9m 3n9n 3n9o 3n9p 3n9q 3puq

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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