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(-) Description

Title :  SOLUTION STRUCTURE OF THE COILED-COIL COMPLEX BETWEEN MBD2 AND P66ALPHA
 
Authors :  D. C. Williams Jr. , N. Scarsdale Jr.
Date :  20 Aug 10  (Deposition) - 04 May 11  (Release) - 24 Aug 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Dna Methylation, Coiled-Coil, Nurd, Mbd2, P66Alpha, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. N. Gnanapragasam, J. N. Scarsdale, M. L. Amaya, H. D. Webb, M. A. Desai, N. M. Walavalkar, S. Z. Wang, S. Zu Zhu, G. D. Ginder, D. C. Williams
P66Alpha-Mbd2 Coiled-Coil Interaction And Recruitment Of Mi-2 Are Critical For Globin Gene Silencing By The Mbd2-Nur Complex.
Proc. Natl. Acad. Sci. Usa V. 108 7487 2011
PubMed-ID: 21490301  |  Reference-DOI: 10.1073/PNAS.1015341108

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REPRESSOR P66-ALPHA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: P66-ALPHA COILED-COIL DOMAIN (UNP RESIDUES 137-178)
    Gene: GATAD2A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HP66ALPHA, GATA ZINC FINGER DOMAIN-CONTAINING PROTEIN 2A
 
Molecule 2 - METHYL-CPG-BINDING DOMAIN PROTEIN 2
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: MBD2 COILED-COIL DOMAIN (UNP RESIDUES 360-393)
    Gene: MBD2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: METHYL-CPG-BINDING PROTEIN MBD2, DEMETHYLASE, DMTASE

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x): AB
NMR Structure * (1x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2L2L)

(-) Sites  (0, 0)

(no "Site" information available for 2L2L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2L2L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2L2L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2L2L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2L2L)

(-) Exons   (0, 0)

(no "Exon" information available for 2L2L)

(-) 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:43
 aligned with P66A_HUMAN | Q86YP4 from UniProtKB/Swiss-Prot  Length:633

    Alignment length:43
                                   145       155       165       175   
           P66A_HUMAN   136 SSPEERERMIKQLKEELRLEEAKLVLLKKLRQSQIQKEATAQK 178
               SCOP domains ------------------------------------------- SCOP domains
               CATH domains ------------------------------------------- CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 2l2l A 136 GSPEERERMIKQLKEELRLEEAKLVLLKKLRQSQIQKEATAQK 178
                                   145       155       165       175   


Chain B from PDB  Type:PROTEIN  Length:36
 aligned with MBD2_HUMAN | Q9UBB5 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:79
                                   324       334       344       354       364       374       384         
           MBD2_HUMAN   315 GSNDETLLSAVASALHTSSAPITGQVSAAVEKNPAVWLNTSQPLCKAFIVTDEDIRKQEERVQQVRKKLEEALMADILS 393
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------MBD_C-2l2lB01 B:211-238     ------ Pfam domains
         Sec.struct. author ..-------------------------------------------.....hhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 2l2l B 209 GS-------------------------------------------KAFIVTDEDIRKQEERVQQVRKKLEEALMADILS 244
                             |       -         -         -         -     | 215       225       235         
                             |                                         211                                 
                           210
   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 2L2L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2L2L)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: MBD_C] (1)

(-) Gene Ontology  (40, 47)

NMR Structure(hide GO term definitions)
Chain A   (P66A_HUMAN | Q86YP4)
molecular function
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    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:0006306    DNA methylation    The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
    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: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: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:0016581    NuRD complex    An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    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.

Chain B   (MBD2_HUMAN | Q9UBB5)
molecular function
    GO:0070742    C2H2 zinc finger domain binding    Interacting selectively and non-covalently with a C2H2-type zinc finger domain of a protein. The C2H2 zinc finger is the classical zinc finger domain, in which two conserved cysteines and histidines co-ordinate a zinc ion.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0000980    RNA polymerase II distal enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
    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:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0008327    methyl-CpG binding    Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide.
    GO:0031492    nucleosomal DNA binding    Interacting selectively and non-covalently with the DNA portion of a nucleosome.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0003696    satellite DNA binding    Interacting selectively and non-covalently with satellite DNA, the many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
    GO:0035197    siRNA binding    Interacting selectively and non-covalently with a small interfering RNA, a 21-23 nucleotide RNA that is processed from double stranded RNA (dsRNA) by an RNAse enzyme.
biological process
    GO:0043044    ATP-dependent chromatin remodeling    Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors.
    GO:0043623    cellular protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell.
    GO:0000183    chromatin silencing at rDNA    Repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0042711    maternal behavior    Female behaviors associated with the care and rearing of offspring.
    GO:0006346    methylation-dependent chromatin silencing    Repression of transcription by methylation of DNA, leading to the formation of heterochromatin.
    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: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:0030177    positive regulation of Wnt signaling pathway    Any process that activates or increases the frequency, rate or extent of Wnt signal transduction.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    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:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000792    heterochromatin    A compact and highly condensed form of chromatin.
    GO:0000118    histone deacetylase complex    A protein complex that possesses histone deacetylase activity.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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