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Title :  MODEL OF EZH2 SET DOMAIN
 
Authors :  S. Warrier, S. Sridhar, G. R. Kumar
Date :  14 Nov 05  (Deposition) - 17 Nov 05  (Release) - 17 Nov 05  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Set Domain, Pcg Protein, Methyltransferase, Tumor Biomarker, A-Binding, Nuclear Protein, Phosphorylation, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Warrier, S. Sridhar, G. R. Kumar
Model Of Ezh2 Set Domain
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENHANCER OF ZESTE HOMOLOG 2
    ChainsA
    FragmentSET DOMAIN, RESIDUES 508-615, 617-734
    OrganHEART, INTESTINE,RESPIRATORY TRACT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymEZH2, ENX-1
    TissueEPITHELIAL

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2C6V)

(-) Sites  (0, 0)

(no "Site" information available for 2C6V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C6V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2C6V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (16, 16)

Theoretical Model (16, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_078324C571WEZH2_HUMANUnclassified  ---AC64W
02UniProtVAR_078325V621MEZH2_HUMANUnclassified (WVS)587783625AV113M
03UniProtVAR_067228Y641CEZH2_HUMANUnclassified  ---AY133C
04UniProtVAR_067229Y641FEZH2_HUMANPolymorphism267601394AY133F
05UniProtVAR_067230Y641HEZH2_HUMANPolymorphism267601395AY133H
06UniProtVAR_067231Y641NEZH2_HUMANUnclassified  ---AY133N
07UniProtVAR_067232Y641SEZH2_HUMANUnclassified  ---AY133S
08UniProtVAR_078326Y658NEZH2_HUMANDisease (WVS)  ---AY150N
09UniProtVAR_078327A677GEZH2_HUMANUnclassified  ---AA169G
10UniProtVAR_078328A677TEZH2_HUMANDisease (WVS)397515547AA169T
11UniProtVAR_078329R679CEZH2_HUMANDisease (WVS)587783626AR171C
12UniProtVAR_078330R685CEZH2_HUMANUnclassified  ---AR177C
13UniProtVAR_067233R685HEZH2_HUMANUnclassified  ---AR177H
14UniProtVAR_067597H689YEZH2_HUMANDisease (WVS)193921147AH181Y
15UniProtVAR_078331S690LEZH2_HUMANDisease (WVS)  ---AS182L
16UniProtVAR_078332Y726DEZH2_HUMANUnclassified  ---AY218D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.EZH2_HUMAN612-727  1A:105-219

(-) Exons   (0, 0)

(no "Exon" information available for 2C6V)

(-) Sequences/Alignments

Theoretical Model
   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:226
 aligned with EZH2_HUMAN | Q15910 from UniProtKB/Swiss-Prot  Length:746

    Alignment length:227
                                   517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       
           EZH2_HUMAN   508 LKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQNFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVSCKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGEELFFDYRYSQADAL 734
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............ee.......................................hhhhh....................eee...........hhhhhhhhh....-......................eeee...eeeehhhhhhhhhhh.......eee....eeee...eehhhhhhee.....eeeeeee.....eeeeee..........ee.......... Sec.struct. author
             SAPs(SNPs) (1) ---------------------------------------------------------------W-------------------------------------------------M-------------------C----------------N------------------G-C-----C---YL-----------------------------------D-------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------F-----------------------------------T-------H------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -------------------------------------------------------------------------------------------------------------------------------------H--------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) -------------------------------------------------------------------------------------------------------------------------------------N--------------------------------------------------------------------------------------------- SAPs(SNPs) (4)
             SAPs(SNPs) (5) -------------------------------------------------------------------------------------------------------------------------------------S--------------------------------------------------------------------------------------------- SAPs(SNPs) (5)
                    PROSITE --------------------------------------------------------------------------------------------------------SET  PDB: A:105-219 UniProt: 612-727                                                                                ------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c6v A   1 LKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQNFCEKFCQCSSECQNRFPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVSCKNCSIQRGSKKH-LLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGEELFFDYRYSQADAL 226
                                    10        20        30        40        50        60        70        80        90       100     | 109       119       129       139       149       159       169       179       189       199       209       219       
                                                                                                                                   106 |                                                                                                                       
                                                                                                                                     107                                                                                                                       

   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 2C6V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2C6V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C6V)

(-) Gene Ontology  (59, 59)

Theoretical Model(hide GO term definitions)
Chain A   (EZH2_HUMAN | Q15910)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0001047    core promoter binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    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:0046976    histone methyltransferase activity (H3-K27 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 27) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 27). This reaction is the addition of a methyl group onto lysine at position 27 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:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:1990841    promoter-specific chromatin binding    Interacting selectively and non-covalently with a section of chromatin that is associated with gene promoter sequences of DNA.
    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:0016279    protein-lysine N-methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue in a protein substrate.
    GO:0000975    regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair.
    GO:0043021    ribonucleoprotein complex binding    Interacting selectively and non-covalently with any complex of RNA and protein.
    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: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.
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:0070314    G1 to G0 transition    A cell cycle arrest process that results in arrest during G1 phase, whereupon the cell enters a specialized resting state known as G0 or quiescence.
    GO:0070301    cellular response to hydrogen peroxide    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 a hydrogen peroxide (H2O2) stimulus.
    GO:0021695    cerebellar cortex development    The process whose specific outcome is the progression of the cerebellar cortex over time, from its formation to the mature structure. The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function.
    GO:0006325    chromatin organization    Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
    GO:0021766    hippocampus development    The progression of the hippocampus over time from its initial formation until its mature state.
    GO:0070734    histone H3-K27 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 27 of the histone.
    GO:0016571    histone methylation    The modification of histones by addition of methyl groups.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:2000134    negative regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that prevents the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    GO:0045605    negative regulation of epidermal cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal cell differentiation.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0045814    negative regulation of gene expression, epigenetic    Any epigenetic process that stops, prevents or reduces the rate of gene expression.
    GO:0048387    negative regulation of retinoic acid receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of retinoic acid receptor signaling pathway activity.
    GO:0043433    negative regulation of sequence-specific DNA binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0051154    negative regulation of striated muscle cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle cell differentiation.
    GO:0034244    negative regulation of transcription elongation from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
    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:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    GO:1900006    positive regulation of dendrite development    Any process that activates or increases the frequency, rate or extent of dendrite development.
    GO:0010718    positive regulation of epithelial to mesenchymal transition    Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
    GO:0071902    positive regulation of protein serine/threonine kinase activity    Any process that increases the rate, frequency, or extent of protein serine/threonine kinase activity.
    GO:0071168    protein localization to chromatin    Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into chromatin.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0042752    regulation of circadian rhythm    Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0014013    regulation of gliogenesis    Any process that modulates the frequency, rate or extent of gliogenesis, the formation of mature glia.
    GO:0050767    regulation of neurogenesis    Any process that modulates the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
    GO:0001932    regulation of protein phosphorylation    Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates 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:0032355    response to estradiol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    GO:0014834    skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration    Any process by which the number of skeletal muscle satellite cells in a skeletal muscle is maintained during muscle regeneration. There are at least three mechanisms by which this is achieved. Skeletal muscle satellite stem cell asymmetric division ensures satellite stem cell numbers are kept constant. Symmetric division of these cells amplifies the number of skeletal muscle satellite stem cells. Some adult skeletal muscle myoblasts (descendants of activated satellite cells) can develop back into quiescent satellite cells, replenishing the overall pool of satellite cells.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0035098    ESC/E(Z) complex    A multimeric protein complex that can methylate lysine-27 and lysine-9 residues of histone H3. In Drosophila the core subunits of the complex include ESC, E(Z), CAF1 (NURF-55) and SU(Z)12. In mammals the core subunits of the complex include EED, EZH2, SUZ12 and RBBP4.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0045120    pronucleus    The nucleus of either the ovum or the spermatozoon following fertilization. Thus, in the fertilized ovum, there are two pronuclei, one originating from the ovum, the other from the spermatozoon that brought about fertilization; they approach each other, but do not fuse until just before the first cleavage, when each pronucleus loses its membrane to release its contents.

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 Related Entries

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

UniProtKB/Swiss-Prot
        EZH2_HUMAN | Q159104mi0 4mi5 5gsa 5h14 5h15 5h17 5h19 5h24 5h25 5hyn 5ij7 5ij8 5ls6 5u5t 5u62 5wuk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2C6V)