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(-) Description

Title :  SOLUTION STRUCTURE OF THE CLR4 CHROMO DOMAIN
 
Authors :  D. A. Horita, A. V. Ivanova, A. S. Altieri, A. J. Klar, R. A. Byrd
Date :  08 Nov 00  (Deposition) - 04 Apr 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (25x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Horita, A. V. Ivanova, A. S. Altieri, A. J. Klar, R. A. Byrd
Solution Structure, Domain Features, And Structural Implications Of Mutants Of The Chromo Domain From The Fission Yeast Histone Methyltransferase Clr4.
J. Mol. Biol. V. 307 861 2001
PubMed-ID: 11273706  |  Reference-DOI: 10.1006/JMBI.2001.4515
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CLR4 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMAL-C2X
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CHROMO DOMAIN, RESIDUES 2-69
    Gene: CLR4
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896

 Structural Features

(-) Chains, Units

  
NMR Structure (25x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1G6Z)

(-) Sites  (0, 0)

(no "Site" information available for 1G6Z)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G6Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1G6Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G6Z)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CLR4_SCHPO8-69  1A:8-69
2CHROMO_1PS00598 Chromo domain signature.CLR4_SCHPO27-47  1A:27-47

(-) Exons   (0, 0)

(no "Exon" information available for 1G6Z)

(-) 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:70
 aligned with CLR4_SCHPO | O60016 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:70
                             1                                                                    
                             |       9        19        29        39        49        59        69
            CLR4_SCHPO    - -MSPKQEEYEVERIVDEKLDRNGAVKLYRIRWLNYSSRSDTWEPPENLSGCSAVLAEWKRRKRRLKGSNS 69
               SCOP domains d1g6za_ A: Histone methyltransferase clr4, chromo domain               SCOP domains
               CATH domains 1g6zA00 A:-2-69  [code=2.40.50.40, no name defined]                    CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eee........eeee..........eeehhhhhh.hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------CHROMO_2  PDB: A:8-69 UniProt: 8-69                            PROSITE (1)
                PROSITE (2) ---------------------------CHROMO_1  PDB: A:27-4---------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------- Transcript
                  1g6z A -2 ISSPKQEEYEVERIVDEKLDRNGAVKLYRIRWLNYSSRSDTWEPPENLSGCSAVLAEWKRRKRRLKGSNS 69
                             ||      9        19        29        39        49        59        69
                             ||                                                                   
                            -1|                                                                   
                              2
   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  (1, 1)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G6Z)

(-) Gene Ontology  (40, 40)

NMR Structure(hide GO term definitions)
Chain A   (CLR4_SCHPO | O60016)
molecular function
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0042054    histone methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone = S-adenosyl-L-homocysteine + methyl-histone. Histone methylation generally occurs on either an arginine or lysine residue.
    GO:0046974    histone methyltransferase activity (H3-K9 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 9) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 9). This reaction is the addition of a methyl group onto lysine at position 9 of the histone H3 protein.
    GO:0018024    histone-lysine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
    GO:0003727    single-stranded RNA binding    Interacting selectively and non-covalently with single-stranded RNA.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0034613    cellular protein localization    Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0030702    chromatin silencing at centromere    Repression of transcription of centromeric DNA by altering the structure of chromatin.
    GO:1990141    chromatin silencing at centromere outer repeat region    Repression of transcription of DNA at the outer repeat region of a regional centromere by altering the structure of chromatin.
    GO:0000183    chromatin silencing at rDNA    Repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0030466    chromatin silencing at silent mating-type cassette    Repression of transcription at silent mating-type loci by alteration of the structure of chromatin.
    GO:0006348    chromatin silencing at telomere    Repression of transcription of telomeric DNA by altering the structure of chromatin.
    GO:0031048    chromatin silencing by small RNA    Repression of transcription by conversion of large regions of DNA into heterochromatin, directed by small RNAs sharing sequence identity to the repressed region.
    GO:0007535    donor selection    The process that determines which donor locus a cell uses, in preference to another, in mating type switching.
    GO:1902368    heterochromatin maintenance involved in chromatin silencing at centromere outer repeat region    Any heterochromatin maintenance that is involved in chromatin silencing at centromere outer repeat region.
    GO:0051567    histone H3-K9 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 9 of the histone.
    GO:0034968    histone lysine methylation    The modification of a histone by addition of one or more methyl groups to a lysine residue.
    GO:0045141    meiotic telomere clustering    The cell cycle process in which the dynamic reorganization of telomeres occurs in early meiotic prophase, during which meiotic chromosome ends are gathered in a bouquet arrangement at the inner surface of the nuclear envelope proximal to the spindle pole body. This plays an important role in progression through meiosis and precedes synapsis.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    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:0090065    regulation of production of siRNA involved in RNA interference    Any process that modulates the frequency, rate or extent of the production of siRNA, the cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of RNA interference.
cellular component
    GO:0043494    CLRC ubiquitin ligase complex    An cullin-dependent E3 ubiquitin ligase/histone H3-K9 methyltransferase complex essential for heterochromatin assembly by RNAi.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0034507    chromosome, centromeric outer repeat region    The portion of the centromeric region of a chromosome that flanks the core region, encompassing repeated regions of a chromosome centromere and the proteins that bind to it.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0031934    mating-type region heterochromatin    Heterochromatic regions of the chromosome found at silenced mating-type loci.
    GO:0044732    mitotic spindle pole body    The microtubule organizing center that forms as part of the mitotic cell cycle; functionally homologous to the animal cell centrosome.
    GO:0031618    nuclear pericentric heterochromatin    Nuclear heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.
    GO:1990707    nuclear subtelomeric heterochromatin    Heterochromatic regions of the chromosome found at the subtelomeric regions of a chromosome in the nucleus.
    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:0005816    spindle pole body    The microtubule organizing center in fungi; functionally homologous to the animal cell centrosome.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CLR4_SCHPO | O60016: 1mvh 1mvx

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