2YPD - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE JUMONJI DOMAIN OF HUMAN JUMONJI DOMAIN CONTAINING 1C PROTEIN

Authors :   M. Vollmar, C. Johansson, T. Krojer, G. Berridge, N. Burgess-Brown, C. Strain-Damerell, S. Froese, E. Williams, S. Goubin, D. Coutandin, F. Von Delft, C. H. Arrowsmith, C. Bountra, A. Edwards, U. Oppermann

Date :   30 Oct 12 (Deposition) - 12 Dec 12 (Release) - 17 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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, C. Strain-Damerell, S. Froese, E. Williams, D. Coutandin, F. Von Delft, J. Weigelt, C. H. Arrowsmith C. Bountra, A. Edwards, U. Oppermann
Crystal Structure Of The Jumonji Domain Of Human Jumonji Domain Containing 1C Protein
To Be Published
PubMed: search

Molecule 1 - PROBABLE JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROT EIN 2C
	Chains	:	A, B
	EC Number	:	1.14.11.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-CTHF
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3-PRARE2
	Expression System Vector Type	:	PLASMID
	Fragment	:	JUMONJI DOMAIN, RESIDUES 2157-2540
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	JUMONJI DOMAIN-CONTAINING PROTEIN 1C, THYROID RECEPTOR-INTERACTING PROTEIN 8, TR-INTERACTING PROTEIN 8, TRIP-8

		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, 13)

No.	Name	Count	Type	Full Name
1	EMT	11	Ligand/Ion	2-(ETHYLMERCURI-THIO)-BENZOIC ACID
2	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	EMT	6	Ligand/Ion	2-(ETHYLMERCURI-THIO)-BENZOIC ACID
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	EMT	5	Ligand/Ion	2-(ETHYLMERCURI-THIO)-BENZOIC ACID
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:2163 , HIS A:2166 , ARG A:2446 , THR A:2447 , CYS A:2448 , EMT A:3499	BINDING SITE FOR RESIDUE EMT A3498
02	AC2	SOFTWARE	HOH A:2096 , HIS A:2166 , ILE A:2393 , ARG A:2446 , CYS A:2448 , EMT A:3498	BINDING SITE FOR RESIDUE EMT A3499
03	AC3	SOFTWARE	GLU A:2184 , CYS A:2185 , GLN A:2188	BINDING SITE FOR RESIDUE EMT A3500
04	AC4	SOFTWARE	HIS B:2166 , ILE B:2393 , ARG B:2446 , CYS B:2448 , EMT B:3499	BINDING SITE FOR RESIDUE EMT B3498
05	AC5	SOFTWARE	CYS B:2163 , HIS B:2166 , ARG B:2446 , THR B:2447 , CYS B:2448 , EMT B:3498	BINDING SITE FOR RESIDUE EMT B3499
06	AC6	SOFTWARE	GLU B:2184 , CYS B:2185 , GLN B:2188 , GLN B:2190	BINDING SITE FOR RESIDUE EMT B3500
07	AC7	SOFTWARE	CYS A:2225 , LYS A:2260 , GLY A:2331 , THR A:2332 , ASN A:2334	BINDING SITE FOR RESIDUE EMT A3501
08	AC8	SOFTWARE	HOH A:2071 , LYS A:2260 , ASP A:2263 , CYS A:2317 , EMT A:3503	BINDING SITE FOR RESIDUE EMT A3502
09	AC9	SOFTWARE	ASP B:2263 , ARG B:2315 , CYS B:2317 , GLN B:2476 , THR B:2478	BINDING SITE FOR RESIDUE EMT B3501
10	BC1	SOFTWARE	CYS B:2317 , THR B:2333 , ASN B:2344 , GLN B:2476	BINDING SITE FOR RESIDUE EMT B3502
11	BC2	SOFTWARE	CYS A:2317 , THR A:2333 , GLN A:2476 , EMT A:3502	BINDING SITE FOR RESIDUE EMT A3503
12	BC3	SOFTWARE	MET B:2274 , PRO B:2275 , ALA B:2276 , ARG B:2277	BINDING SITE FOR RESIDUE NA B3503
13	BC4	SOFTWARE	MET A:2274 , ALA A:2276 , ARG A:2277	BINDING SITE FOR RESIDUE NA A3504

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

Asymmetric Unit

No.	Residues
1	Trp A:2264	-	Pro A:2265
2	Trp B:2264	-	Pro B:2265

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049658	D	2400	E	JHD2C_HUMAN	Polymorphism	34491125	A/B	D	2400	E

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_049658	D	2400	E	JHD2C_HUMAN	Polymorphism	34491125	A	D	2400	E

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_049658	D	2400	E	JHD2C_HUMAN	Polymorphism	34491125	B	D	2400	E

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.	JHD2C_HUMAN	2274-2498	2	A:2274-2497 B:2274-2497

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJC	PS51184	JmjC domain profile.	JHD2C_HUMAN	2274-2498	1	A:2274-2497 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJC	PS51184	JmjC domain profile.	JHD2C_HUMAN	2274-2498	1	- B:2274-2497

(no "Exon" information available for 2YPD)

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:327
 aligned with JHD2C_HUMAN | Q15652 from UniProtKB/Swiss-Prot  Length:2540

    Alignment length:342
                                  2165      2175      2185      2195      2205      2215      2225      2235      2245      2255      2265      2275      2285      2295      2305      2315      2325      2335      2345      2355      2365      2375      2385      2395      2405      2415      2425      2435      2445      2455      2465      2475      2485      2495  
         JHD2C_HUMAN   2156 DIPHSWICEKHILWLKDYKNSSNWKLFKECWKQGQPAVVSGVHKKMNISLWKAESISLDFGDHQADLLNCKDSIISNANVKEFWDGFEEVSKRQKNKSGETVVLKLKDWPSGEDFKTMMPARYEDLLKSLPLPEYCNPEGKFNLASHLPGFFVRPDLGPRLCSAYGVVAAKDHDIGTTNLHIEVSDVVNILVYVGIAKGNGILSKAGILKKFEEEDLDDILRKRLKDSSEIPGALWHIYAGKDVDKIREFLQKISKEQGLEVLPEHDPIRDQSWYVNKKLRQRLLEEYGVRTCTLIQFLGDAIVLPAGALHQVQNFHSCIQVTEDFVSPEHLVESFHLTQEL 2497
               SCOP domains d2ypda_ A: automated matches                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee....eeee......hhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhh......ee.........hhhhhhhh...hhhh------....eee.....hhhhhhhhhhhhhhhhhhh.hhhhhh...........hhhhh.---..eeeee.............eeeee...eeeeeeeeee........hhhhhhhhhhh...hhhhhhhhh.....eeeeeeeehhhhhhhhhhhhhhhhhhhh------.hhhhhh....hhhhhhhhhhhhh...eeeeee...eeee....eeeeee..eeeeeeeee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------E------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------JMJC  PDB: A:2274-2497 UniProt: 2274-2498                                                                                                                                                                                        PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2ypd A    0 MIPHSWICEKHILWLKDYKNSSNWKLFKECWKQGQPAVVSGVHKKMNISLWKAESISLDFGDHQADLLNCKDSIISNANVKEFWDGFEEVSKR------ETVVLKLKDWPSGEDFKTMMPARYEDLLKSLPLPEYCNPEGKFNLASHLPGFFVR---GPRLCSAYGVVAAKDHDIGTTNLHIEVSDVVNILVYVGIAKGNGILSKAGILKKFEEEDLDDILRKRLKDSSEIPGALWHIYAGKDVDKIREFLQKISKEQG------HDPIRDQSWYVNKKLRQRLLEEYGVRTCTLIQFLGDAIVLPAGALHQVQNFHSCIQVTEDFVSPEHLVESFHLTQEL 2497
                            ||    2165      2175      2185      2195      2205      2215      2225      2235      2245  |   2255      2265      2275      2285      2295      2305   |  2315      2325      2335      2345      2355      2365      2375      2385      2395      2405        |-     |2425      2435      2445      2455      2465      2475      2485      2495  
                            ||                                                                                       2248   2255                                                  2309   |                                                                                                 2414   2421                                                                            
                            0|                                                                                                                                                        2313                                                                                                                                                                                        
                          2157

Chain B from PDB  Type:PROTEIN  Length:326
 aligned with JHD2C_HUMAN | Q15652 from UniProtKB/Swiss-Prot  Length:2540

    Alignment length:342
                                  2165      2175      2185      2195      2205      2215      2225      2235      2245      2255      2265      2275      2285      2295      2305      2315      2325      2335      2345      2355      2365      2375      2385      2395      2405      2415      2425      2435      2445      2455      2465      2475      2485      2495  
         JHD2C_HUMAN   2156 DIPHSWICEKHILWLKDYKNSSNWKLFKECWKQGQPAVVSGVHKKMNISLWKAESISLDFGDHQADLLNCKDSIISNANVKEFWDGFEEVSKRQKNKSGETVVLKLKDWPSGEDFKTMMPARYEDLLKSLPLPEYCNPEGKFNLASHLPGFFVRPDLGPRLCSAYGVVAAKDHDIGTTNLHIEVSDVVNILVYVGIAKGNGILSKAGILKKFEEEDLDDILRKRLKDSSEIPGALWHIYAGKDVDKIREFLQKISKEQGLEVLPEHDPIRDQSWYVNKKLRQRLLEEYGVRTCTLIQFLGDAIVLPAGALHQVQNFHSCIQVTEDFVSPEHLVESFHLTQEL 2497
               SCOP domains d2ypdb_ B: automated matches                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee....eeee......hhhhhhhhhhh....eee.hhhhh.hhhhhhhhhhhhhhh......ee.........hhhhhhhh...hhhh------....eee.....hhhhhhhhhhhhhhhhhhh.hhhhhh...........hhhhh----..eeeee.............eeeee...eeeeeeeeee........hhhhhhhhhhh...hhhhhhhhh.....eeeeeeeehhhhhhhhhhhhhhhhhhhh------.hhhhhh....hhhhhhhhhhhhh...eeeeee...eeee....eeeeee..eeeeeeeee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------E------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------JMJC  PDB: B:2274-2497 UniProt: 2274-2498                                                                                                                                                                                        PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2ypd B    0 MIPHSWICEKHILWLKDYKNSSNWKLFKECWKQGQPAVVSGVHKKMNISLWKAESISLDFGDHQADLLNCKDSIISNANVKEFWDGFEEVSKR------ETVVLKLKDWPSGEDFKTMMPARYEDLLKSLPLPEYCNPEGKFNLASHLPGFFV----GPRLCSAYGVVAAKDHDIGTTNLHIEVSDVVNILVYVGIAKGNGILSKAGILKKFEEEDLDDILRKRLKDSSEIPGALWHIYAGKDVDKIREFLQKISKEQG------HDPIRDQSWYVNKKLRQRLLEEYGVRTCTLIQFLGDAIVLPAGALHQVQNFHSCIQVTEDFVSPEHLVESFHLTQEL 2497
                            ||    2165      2175      2185      2195      2205      2215      2225      2235      2245  |   2255      2265      2275      2285      2295      2305  |   2315      2325      2335      2345      2355      2365      2375      2385      2395      2405        |-     |2425      2435      2445      2455      2465      2475      2485      2495  
                            0|                                                                                       2248   2255                                                 2308 2313                                                                                                 2414   2421                                                                            
                          2157

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: automated matches (5)

Protein domain: automated matches (5)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d2ypda_	A:
1b	d2ypdb_	B:

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

(no "Pfam Domain" information available for 2YPD)

Asymmetric Unit(hide GO term definitions)

Chain A,B (JHD2C_HUMAN | Q15652)

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: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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046966	thyroid hormone receptor binding	Interacting selectively and non-covalently with a thyroid hormone receptor.
biological process
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	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: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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	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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	2ypd
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	JHD2C_HUMAN \| Q15652	:	5fzo

2ypr	CRYSTAL STRUCTURE OF THE DNA BINDING ETS DOMAIN OF HUMAN PROTEIN FEV

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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