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(-) Description

Title :  STRUCTURE OF SET7/9
 
Authors :  T. W. Kwon, J. H. Chang, Y. Cho
Date :  09 Nov 02  (Deposition) - 04 Feb 03  (Release) - 23 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Ligand Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Kwon, J. H. Chang, E. Kwak, C. W. Lee, A. Joachimiak, Y. C. Kim, J. Lee, Y. Cho
Mechanism Of Histone Lysine Methyl Transfer Revealed By The Structure Of Set7/9-Adomet
Embo J. V. 22 292 2003
PubMed-ID: 12514135  |  Reference-DOI: 10.1093/EMBOJ/CDG025

(-) Compounds

Molecule 1 - SET DOMAIN-CONTAINING PROTEIN 7
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-28A
    Expression System StrainBL21[DE3]
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 70-366
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSET7/9 METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:226 , GLU A:228 , GLY A:264 , ASN A:265 , HIS A:293 , LYS A:294 , ALA A:295 , ASN A:296 , HIS A:297 , TYR A:335 , TRP A:352 , GLU A:356 , HOH A:1021 , HOH A:1049BINDING SITE FOR RESIDUE SAM A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N6C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N6C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N6C)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.SETD7_HUMAN214-336  1A:214-336

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002740311aENSE00001831410chr4:140477928-140477252677SETD7_HUMAN1-14140--
1.3ENST000002740313ENSE00001613109chr4:140468203-140468074130SETD7_HUMAN14-57440--
1.4aENST000002740314aENSE00001643989chr4:140454520-140454319202SETD7_HUMAN57-124681A:79-12446
1.5ENST000002740315ENSE00001671090chr4:140450374-140450185190SETD7_HUMAN125-188641A:125-18864
1.6ENST000002740316ENSE00001802218chr4:140444589-14044450882SETD7_HUMAN188-215281A:188-21528
1.7bENST000002740317bENSE00001663487chr4:140441548-140441431118SETD7_HUMAN215-254401A:215-25440
1.8ENST000002740318ENSE00001734092chr4:140439196-140439039158SETD7_HUMAN255-307531A:255-30753
1.9ENST000002740319ENSE00001192306chr4:140432997-1404271905808SETD7_HUMAN307-366601A:307-363 (gaps)57

(-) Sequences/Alignments

Asymmetric/Biological 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 A from PDB  Type:PROTEIN  Length:283
 aligned with SETD7_HUMAN | Q8WTS6 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:285
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358     
          SETD7_HUMAN    79 GGVLQGTYVDGELNGPAQEYDTDGRLIFKGQYKDNIRHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPGKSGPEAPEWYQVELKAFQAT 363
               SCOP domains d1n6ca1 A:79-193 Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain                                 d1n6ca2 A:194-363 Histone H3 K4-specific methyltransferase SET7/9 catalytic domain                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------1n6cA02 A:194-363 SET domain                                                                                                                                               CATH domains
               Pfam domains ---------------------------MORN-1n6cA01 A:106-128 --------------------------------------------------------------------------------------------------SET-1n6cA02 A:227-336                                                                                         --------------------------- Pfam domains
         Sec.struct. author ...ee..ee..eeeeeeeee.....eeeeeeee..eeeeeeeee.....eeeee........eeeeeee.....eeeeeeee..eeeeeeeeeeeeee..eeeeee.....ee.................hhhhhhheeeee.......eeeee........eeeee..eeehhhhhhhhhhhhh...ee.....eee.hhhhhh.......hhhhhee.....eeeeeeee...eeeeeeee........eeee....--..........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------SET  PDB: A:214-336 UniProt: 214-336                                                                                       --------------------------- PROSITE
           Transcript 1 (1) Exon 1.4a  PDB: A:79-124 UniProt: 57-124      Exon 1.5  PDB: A:125-188 UniProt: 125-188                       --------------------------Exon 1.7b  PDB: A:215-254               Exon 1.8  PDB: A:255-307 UniProt: 255-307            -------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:188-215    -------------------------------------------------------------------------------------------Exon 1.9  PDB: A:307-363 (gaps) UniProt: 307-366          Transcript 1 (2)
                 1n6c A  79 GGVLQGTYVDGELNGPAQEYDTDGRLIFKGQYKDNIRHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGY--SPPGKSGPEAPEWYQVELKAFQAT 363
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328        |- |     348       358     
                                                                                                                                                                                                                                                                                            337  |                       
                                                                                                                                                                                                                                                                                               340                       

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: MORN (14)
(-)
Family: SET (46)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SETD7_HUMAN | Q8WTS6)
molecular function
    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: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:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    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: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:0006974    cellular response to DNA damage 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 a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0070828    heterochromatin organization    Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic heterochromatin, a compact and highly condensed form of chromatin.
    GO:0034968    histone lysine methylation    The modification of a histone by addition of one or more methyl groups to a lysine residue.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0018027    peptidyl-lysine dimethylation    The methylation of peptidyl-lysine to form peptidyl-N6,N6-dimethyl-L-lysine.
    GO:0018022    peptidyl-lysine methylation    The methylation of peptidyl-lysine to form either the mono-, di- or trimethylated derivative.
    GO:0018026    peptidyl-lysine monomethylation    The methylation of peptidyl-lysine to form peptidyl-N6-methyl-L-lysine.
    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:0051570    regulation of histone H3-K9 methylation    Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 9 of histone H3.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045471    response to ethanol    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 an ethanol stimulus.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SETD7_HUMAN | Q8WTS61h3i 1mt6 1muf 1n6a 1o9s 1xqh 2f69 3cbm 3cbo 3cbp 3m53 3m54 3m55 3m56 3m57 3m58 3m59 3m5a 3os5 3vuz 3vv0 4e47 4j7f 4j7i 4j83 4j8o 4jds 4jlg 5ayf 5eg2

(-) Related Entries Specified in the PDB File

1n6a RESIDUES 108-366 OF THE SAME PROTEIN