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Title :   CRYSTAL STRUCTURE OF JMJD5 DOMAIN OF HUMAN LYSINE-SPECIFIC DEMETHYLASE 8 (KDM8) IN COMPLEX WITH N-OXALYLGLYCINE (NOG)

Authors :   M. Vollmar, C. Johansson, T. Krojer, P. Canning, C. Allerston, A. Gadha F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, U. Oppermann

Date :   05 Dec 11 (Deposition) - 29 Feb 12 (Release) - 29 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

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

Reference :   M. Vollmar, C. Johansson, T. Krojer, P. Canning, C. Allerston, A. Gadhave, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, U. Oppermann
Crystal Structure Of Jmjd5 Domain Of Human Lysine- Specific Demethylase 8 (Kdm8) In Complex With N- Oxalylglycine (Nog)
To Be Published
PubMed: search

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 8
	Chains	:	A, B
	EC Number	:	1.14.11.27
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS
	Expression System Vector Type	:	PLASMID
	Fragment	:	JMJD5 DOMAIN, RESIDUES 218-454
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	JMJC DOMAIN-CONTAINING PROTEIN 5, JUMONJI DOMAIN-CONTAINING PROTEIN 5

		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 (2, 6)

No.	Name	Count	Type	Full Name
1	OGA	2	Ligand/Ion	N-OXALYLGLYCINE
2	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	OGA	1	Ligand/Ion	N-OXALYLGLYCINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	OGA	1	Ligand/Ion	N-OXALYLGLYCINE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:359 , ASP A:361 , HIS A:438 , OGA A:501	BINDING SITE FOR RESIDUE ZN A 500
2	AC2	SOFTWARE	TYR A:310 , TRP A:348 , SER A:356 , HIS A:359 , ASP A:361 , ASN A:365 , LYS A:374 , HIS A:438 , VAL A:440 , ZN A:500	BINDING SITE FOR RESIDUE OGA A 501
3	AC3	SOFTWARE	HIS A:252 , ASP A:283 , HIS A:393	BINDING SITE FOR RESIDUE ZN A 502
4	AC4	SOFTWARE	HIS B:359 , ASP B:361 , HIS B:438 , OGA B:501	BINDING SITE FOR RESIDUE ZN B 500
5	AC5	SOFTWARE	TYR B:310 , TRP B:348 , SER B:356 , HIS B:359 , ASP B:361 , ASN B:365 , LYS B:374 , HIS B:438 , VAL B:440 , TRP B:452 , ZN B:500	BINDING SITE FOR RESIDUE OGA B 501
6	AC6	SOFTWARE	HIS B:252 , ASP B:283 , HIS B:393	BINDING SITE FOR RESIDUE ZN B 502

(no "SS Bond" information available for 4AAP)

(no "Cis Peptide Bond" information available for 4AAP)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_032928	E	302	D	KDM8_HUMAN	Polymorphism	34445573	A/B	E	340	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_032928	E	302	D	KDM8_HUMAN	Polymorphism	34445573	A	E	340	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_032928	E	302	D	KDM8_HUMAN	Polymorphism	34445573	B	E	340	D

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJC	PS51184	JmjC domain profile.	KDM8_HUMAN	271-416	2	A:309-454 B:309-454

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJC	PS51184	JmjC domain profile.	KDM8_HUMAN	271-416	1	A:309-454 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJC	PS51184	JmjC domain profile.	KDM8_HUMAN	271-416	1	- B:309-454

(no "Exon" information available for 4AAP)

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:235
 aligned with KDM8_HUMAN | Q8N371 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:238
                                   188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408        
           KDM8_HUMAN   179 KLEKTVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS 416
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee..hhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeehhhhhhhhh..--.....eeeehhhhhhhhhhhhh..hhhhhhh..hhhhheeeeeee....eeeee....eeeeeeee..eeeeeehhhhhhhhh......-.......................eeeeee....eeee....eeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------D------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------JMJC  PDB: A:309-454 UniProt: 271-416                                                                                                              PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aap A   0 MLEKTVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVN--RDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHL-HNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS 454
                            ||     226       236       246       256       266       276       286       296      |306       316       326       336       346       356       366       376       386       396       406       416       426       436       446        
                            ||                                                                                  303  |                                                                                     394 |                                                          
                            0|                                                                                     306                                                                                       396                                                          
                           218

Chain B from PDB  Type:PROTEIN  Length:233
 aligned with KDM8_HUMAN | Q8N371 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:238
                                   188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408        
           KDM8_HUMAN   179 KLEKTVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS 416
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee..hhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeehhhhhhhhh..--.....eeeehhhhhhhhhhh....hhhhhhh..hhhhheeeeeee....eeeee....eeeeeeee..eeeeeehhhhhhhhh.....---......................eeeeee....eeee....eeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------D------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------JMJC  PDB: B:309-454 UniProt: 271-416                                                                                                              PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aap B   0 MLEKTVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVN--RDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTH---NTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS 454
                            ||     226       236       246       256       266       276       286       296      |306       316       326       336       346       356       366       376       386      |  -|      406       416       426       436       446        
                            0|                                                                                  303  |                                                                                    393 397                                                         
                           218                                                                                     306

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 4AAP)

(no "CATH Domain" information available for 4AAP)

(no "Pfam Domain" information available for 4AAP)

Asymmetric Unit(hide GO term definitions)

Chain A,B (KDM8_HUMAN | Q8N371)

molecular function
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	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:0051864	histone demethylase activity (H3-K36 specific)	Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 36) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 36 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.
biological process
	GO:0000086	G2/M transition of mitotic cell cycle	The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0070544	histone H3-K36 demethylation	The modification of histone H3 by the removal of a methyl group from lysine at position 36 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:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	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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	KDM8_HUMAN \| Q8N371	:	3uyj 4gaz 4gjy 4gjz 4qu1 5fbj

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Ligands, Modified Residues, Ions (2, 6)

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