2JRZ - JenaLib

Title :   SOLUTION STRUCTURE OF THE BRIGHT/ARID DOMAIN FROM THE HUMAN JARID1C PROTEIN.

Authors :   C. Koehler, S. Bishop, E. F. Dowler, A. Diehl, P. Schmieder, M. Leidert, M. Sundstrom, C. H. Arrowsmith, J. Wiegelt, A. Edwards, H. Oschkinat, L. J. Ball, Structural Genomics Consortium (Sgc)

Date :   29 Jun 07 (Deposition) - 10 Jul 07 (Release) - 18 Aug 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Jarid1C, Bright/Arid Domain, Helical, Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Koehler, S. Bishop, E. F. Dowler, P. Schmieder, A. Diehl, H. Oschkinat, L. J. Ball
Backbone And Sidechain 1H, 13C And 15N Resonance Assignments Of The Bright/Arid Domain From The Human Jarid1C (Smcx) Protein.
Biomol. Nmr Assign. V. 2 9 2008
PubMed-ID: 19636912 | Reference-DOI: 10.1007/S12104-007-9071-7
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (4, 4)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000375401	1a	ENSE00001038655	X:53254604-53253922	683	KDM5C_HUMAN	1-50	50	0	-	-
1.3	ENST00000375401	3	ENSE00001666724	X:53250098-53250021	78	KDM5C_HUMAN	51-76	26	1	A:1-6	6
1.4d	ENST00000375401	4d	ENSE00001798397	X:53247580-53247458	123	KDM5C_HUMAN	77-117	41	1	A:7-47	41
1.5d	ENST00000375401	5d	ENSE00001691478	X:53247148-53246978	171	KDM5C_HUMAN	118-174	57	1	A:48-104	57
1.6a	ENST00000375401	6a	ENSE00001636291	X:53246459-53246325	135	KDM5C_HUMAN	175-219	45	1	A:105-117	13
1.7	ENST00000375401	7	ENSE00000860393	X:53245379-53245256	124	KDM5C_HUMAN	220-261	42	0	-	-
1.8a	ENST00000375401	8a	ENSE00000860394	X:53245158-53244977	182	KDM5C_HUMAN	261-321	61	0	-	-
1.9	ENST00000375401	9	ENSE00000860395	X:53244029-53243871	159	KDM5C_HUMAN	322-374	53	0	-	-
1.10	ENST00000375401	10	ENSE00001774049	X:53241088-53240969	120	KDM5C_HUMAN	375-414	40	0	-	-
1.11b	ENST00000375401	11b	ENSE00000860397	X:53240837-53240679	159	KDM5C_HUMAN	415-467	53	0	-	-
1.12	ENST00000375401	12	ENSE00001600748	X:53240039-53239858	182	KDM5C_HUMAN	468-528	61	0	-	-
1.13a	ENST00000375401	13a	ENSE00001800989	X:53239758-53239596	163	KDM5C_HUMAN	528-582	55	0	-	-
1.14b	ENST00000375401	14b	ENSE00001724828	X:53231155-53231036	120	KDM5C_HUMAN	583-622	40	0	-	-
1.15a	ENST00000375401	15a	ENSE00000860401	X:53230926-53230732	195	KDM5C_HUMAN	623-687	65	0	-	-
1.16	ENST00000375401	16	ENSE00001763425	X:53228340-53228159	182	KDM5C_HUMAN	688-748	61	0	-	-
1.17a	ENST00000375401	17a	ENSE00001614347	X:53228070-53227946	125	KDM5C_HUMAN	748-790	43	0	-	-
1.17c	ENST00000375401	17c	ENSE00000860404	X:53227819-53227672	148	KDM5C_HUMAN	790-839	50	0	-	-
1.18a	ENST00000375401	18a	ENSE00000860405	X:53227058-53226953	106	KDM5C_HUMAN	839-874	36	0	-	-
1.19	ENST00000375401	19	ENSE00000860406	X:53226226-53225868	359	KDM5C_HUMAN	875-994	120	0	-	-
1.20	ENST00000375401	20	ENSE00001690780	X:53225236-53225098	139	KDM5C_HUMAN	994-1040	47	0	-	-
1.21	ENST00000375401	21	ENSE00001667228	X:53224592-53224413	180	KDM5C_HUMAN	1041-1100	60	0	-	-
1.22	ENST00000375401	22	ENSE00001605274	X:53224250-53224113	138	KDM5C_HUMAN	1101-1146	46	0	-	-
1.23	ENST00000375401	23	ENSE00000860410	X:53223920-53223321	600	KDM5C_HUMAN	1147-1346	200	0	-	-
1.24b	ENST00000375401	24b	ENSE00000860411	X:53223033-53222955	79	KDM5C_HUMAN	1347-1373	27	0	-	-
1.25	ENST00000375401	25	ENSE00001764157	X:53222818-53222619	200	KDM5C_HUMAN	1373-1439	67	0	-	-
1.26c	ENST00000375401	26c	ENSE00001466943	X:53222514-53221334	1181	KDM5C_HUMAN	1440-1560	121	0	-	-

Sequences/Alignments

NMR Structure

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:117
 aligned with KDM5C_HUMAN | P41229 from UniProtKB/Swiss-Prot  Length:1560

    Alignment length:118
                                    80        90       100       110       120       130       140       150       160       170       180        
          KDM5C_HUMAN    71 RLNELEAQTRVKLNYLDQIAKFWEIQGSSLKIPNVERRILDLYSLSKIVVEEGGYEAICKDRRWARVAQRLNYPPGKNIGSLLRSHYERIVYPYEMYQSGANLVQCNTRPFDNEEKDK 188
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2jrzA00 A:1-117  [code=1.10.150.60, no name defined]                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...hhhhhhhhhhhhhhh........ee..ee.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.-....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------G----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------ARID  PDB: A:9-99 UniProt: 79-169                                                          ------------------- PROSITE
               Transcript 1 1.3   Exon 1.4d  PDB: A:7-47 UniProt: 77-117   Exon 1.5d  PDB: A:48-104 UniProt: 118-174                Exon 1.6a      Transcript 1
                 2jrz A   1 SMNELEAQTRVKLNYLDQIAKFWEIQGSSLKIPNVERRILDLYSLSKIVVEEGGYEAICKDRRWARVAQRLNYPPGKNIGSLLRSHYERIVYPYEMYQSGANLV-CNTRPFDNEEKDK 117
                                    10        20        30        40        50        60        70        80        90       100   | | 109        
                                                                                                                                 104 |            
                                                                                                                                   105

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

NMR Structure(hide GO term definitions)

Chain A (KDM5C_HUMAN | P41229)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0032452	histone demethylase activity	Catalysis of the removal of a methyl group from a histone.
	GO:0032453	histone demethylase activity (H3-K4 specific)	Catalysis of the removal of a methyl group from lysine at position 4 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:0016706	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors	Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0034720	histone H3-K4 demethylation	The modification of histone H3 by the removal of a methyl group from lysine at position 4 of the histone.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	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:0048511	rhythmic process	Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	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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