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(-) Description

Title :  SOLUTION STRUCTURE OF JARID1A C-TERMINAL PHD FINGER IN COMPLEX WITH H3(1-9)K4ME3
 
Authors :  J. Song, Z. Wang, D. J. Patel
Date :  12 Mar 09  (Deposition) - 05 May 09  (Release) - 16 Jun 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Phd Finger, Jarid1A, Histone Modification, Leukemia, Alternative Splicing, Chromatin Regulator, Developmental Protein, Dioxygenase, Iron, Metal-Binding, Nucleus, Oxidoreductase, Phosphoprotein, Polymorphism, Transcription, Transcription Regulation, Zinc, Zinc-Finger, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. G. Wang, J. Song, Z. Wang, H. L. Dormann, F. Casadio, H. Li, J. L. Luo, D. J. Patel, C. D. Allis
Haematopoietic Malignancies Caused By Dysregulation Of A Chromatin-Binding Phd Finger.
Nature V. 459 847 2009
PubMed-ID: 19430464  |  Reference-DOI: 10.1038/NATURE08036
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HISTONE DEMETHYLASE JARID1A
    ChainsA
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSFDUET-1
    Expression System StrainROSETTA 2(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPHD-TYPE C-TERMINAL ZINC FINGER
    GeneJARID1A, RBBP2, RBP2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymJUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1A, RETINOBLASTOMA-BINDING PROTEIN 2, RBBP-2
 
Molecule 2 - H3(1-9)K4ME3
    ChainsB
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

NMR Structure (2, 3)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
2ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:21 , CYS A:25 , CYS A:48 , CYS A:51BINDING SITE FOR RESIDUE ZN A 53
2AC2SOFTWARECYS A:3 , CYS A:8 , HIS A:30 , CYS A:33BINDING SITE FOR RESIDUE ZN A 54

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KGI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KGI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2KGI)

(-) Exons   (0, 0)

(no "Exon" information available for 2KGI)

(-) 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:52
 aligned with KDM5A_HUMAN | P29375 from UniProtKB/Swiss-Prot  Length:1690

    Alignment length:52
                                  1617      1627      1637      1647      1657  
         KDM5A_HUMAN   1608 AVCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA 1659
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee.......eee......hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                2kgi A    1 SVCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA   52
                                    10        20        30        40        50  

Chain B from PDB  Type:PROTEIN  Length:9
                                          
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author .eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                2kgi B  301 ARTkQTARK  309
                               |     
                             304-M3L 

   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)

(no "SCOP Domain" information available for 2KGI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (31, 31)

NMR Structure(hide GO term definitions)
Chain A   (KDM5A_HUMAN | P29375)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0031490    chromatin DNA binding    Interacting selectively and non-covalently with DNA that is assembled into chromatin.
    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:0032452    histone demethylase activity    Catalysis of the removal of a methyl group from a histone.
    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: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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0032922    circadian regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
    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:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:1901726    negative regulation of histone deacetylase activity    Any process that stops, prevents or reduces the frequency, rate or extent of histone deacetylase activity.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0019907    cyclin-dependent protein kinase activating kinase holoenzyme complex    A cyclin-dependent kinase activating kinase complex capable of activating cyclin-dependent kinases by threonine phosphorylation, thus regulating cell cycle progression. consists of a kinase, cyclin and optional assembly factors, in human CDK7, CCNH and MNAT1. CAK activity is itself regulated throughout the cell cycle by T-loop phosphorylation of its kinase component (CDK7 in human). Phosphorylation of serine residues during mitosis inactivates the enzyme. Also capable of CAK phosphorylating the carboxyl-terminal domain (CTD) of RNA polymerase II and other transcription activating proteins, as part of the general transcription factor TFIIH.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.
    GO:0032993    protein-DNA complex    A macromolecular complex containing both protein and DNA molecules.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KDM5A_HUMAN | P293752jxj 2kgg 3gl6 5c11 5ceh 5e6h 5isl 5ivb 5ivc 5ive 5ivf 5ivj 5ivv 5ivy 5iw0 5iwf 5k4l 5v9p 5v9t

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