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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HISTONE METHYLTRANSFERASE SET7/9
 
Authors :  J. R. Wilson, C. Jing, P. A. Walker, S. R. Martin, S. A. Howell, G. M. Blackburn, S. J. Gamblin, B. Xiao
Date :  04 Sep 02  (Deposition) - 11 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Methyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Wilson, C. Jing, P. A. Walker, S. R. Martin, S. A. Howell, G. M. Blackburn, S. J. Gamblin, B. Xiao
Crystal Structure And Functional Analysis Of The Histone Methyltransferase Set7/9
Cell(Cambridge, Mass. ) V. 111 105 2002
PubMed-ID: 12372304  |  Reference-DOI: 10.1016/S0092-8674(02)00964-9

(-) Compounds

Molecule 1 - HISTONE H3 LYSINE 4 SPECIFIC METHYLTRANSFERASE
    ChainsA, B
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentN-DOMAIN, SET-DOMAIN, RESIDUES 52-344
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHISTONE H3-K4, METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2133 , HOH A:2134 , HOH A:2147 , HOH A:2149 , HOH A:2150 , HOH B:2119BINDING SITE FOR RESIDUE MG A1345
2AC2SOFTWAREGLU A:279 , HIS A:283 , GLU B:279 , HIS B:283BINDING SITE FOR RESIDUE MG A1346
3AC3SOFTWAREHOH A:2128 , HOH B:2123 , HOH B:2125 , HOH B:2140 , HOH B:2141 , HOH B:2143BINDING SITE FOR RESIDUE MG B1346

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H3I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1H3I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H3I)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.SETD7_HUMAN214-336
 
  2A:214-336
B:214-336
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.SETD7_HUMAN214-336
 
  1A:214-336
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.SETD7_HUMAN214-336
 
  1-
B:214-336

(-) Exons   (7, 14)

Asymmetric Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002740311aENSE00001831410chr4:140477928-140477252677SETD7_HUMAN1-14140--
1.3ENST000002740313ENSE00001613109chr4:140468203-140468074130SETD7_HUMAN14-57442A:52-57
B:52-57
6
6
1.4aENST000002740314aENSE00001643989chr4:140454520-140454319202SETD7_HUMAN57-124682A:57-124
B:57-124
68
68
1.5ENST000002740315ENSE00001671090chr4:140450374-140450185190SETD7_HUMAN125-188642A:125-188
B:125-188
64
64
1.6ENST000002740316ENSE00001802218chr4:140444589-14044450882SETD7_HUMAN188-215282A:188-215
B:188-215
28
28
1.7bENST000002740317bENSE00001663487chr4:140441548-140441431118SETD7_HUMAN215-254402A:215-254
B:215-254
40
40
1.8ENST000002740318ENSE00001734092chr4:140439196-140439039158SETD7_HUMAN255-307532A:255-307
B:255-307
53
53
1.9ENST000002740319ENSE00001192306chr4:140432997-1404271905808SETD7_HUMAN307-366602A:307-344
B:307-344
38
38

(-) 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 A from PDB  Type:PROTEIN  Length:293
 aligned with SETD7_HUMAN | Q8WTS6 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:293
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341   
          SETD7_HUMAN    52 FFFDGSTLEGYYVDDALQGQGVYTYEDGGVLQGTYVDGELNGPAQEYDTDGRLIFKGQYKDNIRHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPGK 344
               SCOP domains d1h3ia1 A:52-193 Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain                                                            d1h3ia2 A:194-344 Histone H3 K4-specific methyltransferase SET7/9 catalytic domain                                                                      SCOP domains
               CATH domains --------1h3iA01 A:60-193 Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain                                                    1h3iA02 A:194-340 SET domain                                                                                                                       ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee..eeeeeeeee.....eeeeeee..eeeeeeeee.....eeeeeeee..ee..eeeee.....eeeee........eeeeeee.....eeeeeeee..eeeeeeeeeeee..................................hhhhhh.eeeee.......eeeee........eeeee..eeehhhhhhhhhhhhh..eee.....eee..............hhhhheee....eeeeeeee...eeeeeeee........eeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------SET  PDB: A:214-336 UniProt: 214-336                                                                                       -------- PROSITE
           Transcript 1 (1) 1.3   -------------------------------------------------------------------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 1.4a  PDB: A:57-124 UniProt: 57-124                            ---------------------------------------------------------------Exon 1.6  PDB: A:188-215    -------------------------------------------------------------------------------------------Exon 1.9  PDB: A:307-344 [INCOMPLETE]  Transcript 1 (2)
                 1h3i A  52 FFFDGSTLEGYYVDDALQGQGVYTYEDGGVLQGTYVDGELNGPAQEYDTDGRLIFKGQYKDNIRHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPGK 344
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341   

Chain B from PDB  Type:PROTEIN  Length:293
 aligned with SETD7_HUMAN | Q8WTS6 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:293
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341   
          SETD7_HUMAN    52 FFFDGSTLEGYYVDDALQGQGVYTYEDGGVLQGTYVDGELNGPAQEYDTDGRLIFKGQYKDNIRHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPGK 344
               SCOP domains d1h3ib1 B:52-193 Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain                                                            d1h3ib2 B:194-344 Histone H3 K4-specific methyltransferase SET7/9 catalytic domain                                                                      SCOP domains
               CATH domains --------1h3iB01 B:60-193 Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain                                                    1h3iB02 B:194-340 SET domain                                                                                                                       ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee..eeeeeeeee.....eeeeeee..eeeeeeeee.....eeeeeeee..ee..eeeee.....eeeee........eeeeeee.....eeeeeeee..eeeeeeeeeeeee.................................hhhhhh.eeeee.......eeeee........eeeee..eeehhhhhhhhhhhhh..eee.....eee..............hhhhheee....eeeeeeee...eeeeeeee........eeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------SET  PDB: B:214-336 UniProt: 214-336                                                                                       -------- PROSITE
           Transcript 1 (1) 1.3   -------------------------------------------------------------------Exon 1.5  PDB: B:125-188 UniProt: 125-188                       --------------------------Exon 1.7b  PDB: B:215-254               Exon 1.8  PDB: B:255-307 UniProt: 255-307            ------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.4a  PDB: B:57-124 UniProt: 57-124                            ---------------------------------------------------------------Exon 1.6  PDB: B:188-215    -------------------------------------------------------------------------------------------Exon 1.9  PDB: B:307-344 [INCOMPLETE]  Transcript 1 (2)
                 1h3i B  52 FFFDGSTLEGYYVDDALQGQGVYTYEDGGVLQGTYVDGELNGPAQEYDTDGRLIFKGQYKDNIRHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPGK 344
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341   

   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, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H3I)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 | Q8WTS61mt6 1muf 1n6a 1n6c 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

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