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(-) Description

Title :  MECHANISM OF RECRUITMENT OF CLASS II HISTONE DEACETYLASES BY MYOCYTE ENHANCER FACTOR-2
 
Authors :  L. Chen, A. Han, J. He, Y. Wu, J. O. Liu
Date :  17 Jun 04  (Deposition) - 21 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  C,D,E,F,P,Q,R,S,X,Y
Biol. Unit 1:  C,D,P,Q,X  (1x)
Biol. Unit 2:  E,F,R,S,Y  (1x)
Keywords :  Mef2, Hdac, Co-Repressor, Transcription, Transcription/Protein Binding/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Han, J. He, Y. Wu, J. O. Liu, L. Chen
Mechanism Of Recruitment Of Class Ii Histone Deacetylases By Myocyte Enhancer Factor-2.
J. Mol. Biol. V. 345 91 2005
PubMed-ID: 15567413  |  Reference-DOI: 10.1016/J.JMB.2004.10.033
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MEF2 BINDING SITE OF NUR77 PROMOTER
    Chains: C, E
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - MEF2 BINDING SITE OF NUR77 PROMOTER
    Chains: D, F
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - MYOCYTE-SPECIFIC ENHANCER FACTOR 2B
    Chains: P, Q, R, S
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: T7
    Fragment: RESIDUES 1-93
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SERUM RESPONSE FACTOR-LIKE PROTEIN 2, XMEF2, RSRFR2
 
Molecule 4 - HISTONE DEACETYLASE 9
    Chains: X, Y
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: T7
    Fragment: RESIDUES 138-158
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: HD9, HD7B, HISTONE DEACETYLASE-RELATED PROTEIN, MEF2-INTERACTING TRANSCRIPTION REPRESSOR MITR

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : CDEFPQRSXY
Biological Unit 1 (1x): CD  PQ  X 
Biological Unit 2 (1x):   EF  RS Y

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1TQE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MADS_BOX_1PS00350 MADS-box domain signature.MEF2B_HUMAN3-57
 
 
 		  4P:3-57
Q:3-57
R:3-57
S:3-57
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MADS_BOX_1PS00350 MADS-box domain signature.MEF2B_HUMAN3-57
 
 
 		  2P:3-57
Q:3-57
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MADS_BOX_1PS00350 MADS-box domain signature.MEF2B_HUMAN3-57
 
 
 		  2-
-
R:3-57
S:3-57

(-) Exons   (0, 0)

(no "Exon" information available for 1TQE)

(-) Sequences/Alignments

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 C from PDB  Type:DNA  Length:17
                                                 
                 1tqe C   1 AAAGCTATTTATAAGCA  17
                                    10       


Chain D from PDB  Type:DNA  Length:17
                                                 
                 1tqe D   1 TTGCTTATAAATAGCTT  17
                                    10       


Chain E from PDB  Type:DNA  Length:17
                                                 
                 1tqe E   1 AAAGCTATTTATAAGCA  17
                                    10       


Chain F from PDB  Type:DNA  Length:17
                                                 
                 1tqe F   1 TTGCTTATAAATAGCTT  17
                                    10       


Chain P from PDB  Type:PROTEIN  Length:90
 aligned with MEF2B_HUMAN | Q02080 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:90
                                    11        21        31        41        51        61        71        81        91
          MEF2B_HUMAN     2 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDMDRVLLKYTEYSEPHESRTNTDILETLKRR  91
               SCOP domains d1tqep_ P: Myocyte enhancer factor Mef2b core                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeee..hhhhhhhhhhhh.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -MADS_BOX_1  PDB: P:3-57 UniProt: 3-57                  ---------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 1tqe P   2 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDMDRVLLKYTEYSEPHESRTNTDILETLKRR  91
                                    11        21        31        41        51        61        71        81        91


Chain Q from PDB  Type:PROTEIN  Length:90
 aligned with MEF2B_HUMAN | Q02080 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:90
                                    11        21        31        41        51        61        71        81        91
          MEF2B_HUMAN     2 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDMDRVLLKYTEYSEPHESRTNTDILETLKRR  91
               SCOP domains d1tqeq_ Q: Myocyte enhancer factor Mef2b core                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeee..hhhhhhhhhhh.....eeehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -MADS_BOX_1  PDB: Q:3-57 UniProt: 3-57                  ---------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 1tqe Q   2 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDMDRVLLKYTEYSEPHESRTNTDILETLKRR  91
                                    11        21        31        41        51        61        71        81        91


Chain R from PDB  Type:PROTEIN  Length:90
 aligned with MEF2B_HUMAN | Q02080 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:90
                                    11        21        31        41        51        61        71        81        91
          MEF2B_HUMAN     2 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDMDRVLLKYTEYSEPHESRTNTDILETLKRR  91
               SCOP domains d1tqer_ R: Myocyte enhancer factor Mef2b core                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeee..hhhhhhhhhhhh.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -MADS_BOX_1  PDB: R:3-57 UniProt: 3-57                  ---------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 1tqe R   2 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDMDRVLLKYTEYSEPHESRTNTDILETLKRR  91
                                    11        21        31        41        51        61        71        81        91


Chain S from PDB  Type:PROTEIN  Length:90
 aligned with MEF2B_HUMAN | Q02080 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:90
                                    11        21        31        41        51        61        71        81        91
          MEF2B_HUMAN     2 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDMDRVLLKYTEYSEPHESRTNTDILETLKRR  91
               SCOP domains d1tqes_ S: Myocyte enhancer factor Mef2b core                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------SRF-TF-1tqeS01 S:9-59                              -------------------------------- Pfam domains (1)
           Pfam domains (2) -------SRF-TF-1tqeS02 S:9-59                              -------------------------------- Pfam domains (2)
           Pfam domains (3) -------SRF-TF-1tqeS03 S:9-59                              -------------------------------- Pfam domains (3)
           Pfam domains (4) -------SRF-TF-1tqeS04 S:9-59                              -------------------------------- Pfam domains (4)
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeee..hhhhhhhhhhh.....eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -MADS_BOX_1  PDB: S:3-57 UniProt: 3-57                  ---------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 1tqe S   2 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDMDRVLLKYTEYSEPHESRTNTDILETLKRR  91
                                    11        21        31        41        51        61        71        81        91


Chain X from PDB  Type:PROTEIN  Length:23
 aligned with HDAC9_MOUSE | Q99N13 from UniProtKB/Swiss-Prot  Length:588

    Alignment length:31
                                   134       144       154 
          HDAC9_MOUSE   125 PPLRGKDRGRERAVASTEVKQKLQEFLLSKS 155
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author ..---....-----...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                 1tqe X 103 SP---KGTG-----ASTEVKQKLQEFLLSKS 125
                             |   |  |-    |  114       124 
                             | 105  |   109                
                           104    108                      


Chain Y from PDB  Type:PROTEIN  Length:23
 aligned with HDAC9_MOUSE | Q99N13 from UniProtKB/Swiss-Prot  Length:588

    Alignment length:31
                                   134       144       154 
          HDAC9_MOUSE   125 PPLRGKDRGRERAVASTEVKQKLQEFLLSKS 155
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author ..---....-----...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                 1tqe Y 103 SP---KGTG-----ASTEVKQKLQEFLLSKS 125
                             |   |  |-    |  114       124 
                           104 105  |   109                
                                  108
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1TQE)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: SRF-TF] (4)

(-) Gene Ontology  (40, 45)

Asymmetric Unit(hide GO term definitions)
Chain P,Q,R,S   (MEF2B_HUMAN | Q02080)
molecular function
    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:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    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:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific 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 (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
    GO:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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: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:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Chain X,Y   (HDAC9_MOUSE | Q99N13)
molecular function
    GO:0004407    histone deacetylase activity    Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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:0033558    protein deacetylase activity    Catalysis of the hydrolysis of an acetyl group or groups from a protein substrate.
    GO:0005080    protein kinase C binding    Interacting selectively and non-covalently with protein kinase C.
    GO:0070491    repressing transcription factor binding    Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0042113    B cell activation    The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    GO:0032869    cellular response to insulin stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0070932    histone H3 deacetylation    The modification of histone H3 by the removal of one or more acetyl groups.
    GO:0070933    histone H4 deacetylation    The modification of histone H4 by the removal of one or more acetyl groups.
    GO:0016575    histone deacetylation    The modification of histones by removal of acetyl groups.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045843    negative regulation of striated muscle tissue development    Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle development.
    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:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0034983    peptidyl-lysine deacetylation    The removal of an acetyl group from an acetylated lysine residue in a peptide or protein.
    GO:0090050    positive regulation of cell migration involved in sprouting angiogenesis    Any process that increases the frequency, rate or extent of cell migration involved in sprouting angiogenesis. Cell migration involved in sprouting angiogenesis is the orderly movement of endothelial cells into the extracellular matrix in order to form new blood vessels contributing to the process of sprouting angiogenesis.
    GO:0048742    regulation of skeletal muscle fiber development    Any process that modulates the frequency, rate or extent of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
    GO:0051153    regulation of striated muscle cell differentiation    Any process that modulates the frequency, rate or extent of striated muscle cell differentiation.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000118    histone deacetylase complex    A protein complex that possesses histone deacetylase activity.
    GO:0035097    histone methyltransferase complex    A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins.
    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:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MEF2B_HUMAN | Q02080: 1n6j

(-) Related Entries Specified in the PDB File

1egw CRYSTAL STRUCTURE OF MEF2A CORE BOUND TO DNA AT 1.5 RESOLUTION
1n6j THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF MYOCYTE ENHANCER FACTOR-2 AND CO-REPRESSOR CABIN1