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(-) Description

Title :  HUMAN EUCHROMATIC HISTONE METHYLTRANSFERASE 1
 
Authors :  J. Min, H. Wu, T. Antoshenko, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (Sgc)
Date :  23 Sep 06  (Deposition) - 24 Oct 06  (Release) - 02 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Euchromatic Histone Methyltransferase 1, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Wu, J. Min, V. V. Lunin, T. Antoshenko, L. Dombrovski, H. Zeng, A. Allali-Hassani, V. Campagna-Slater, M. Vedadi, C. H. Arrowsmith, A. N. Plotnikov, M. Schapira
Structural Biology Of Human H3K9 Methyltransferases
Plos One V. 5 E8570 2010
PubMed-ID: 20084102  |  Reference-DOI: 10.1371/JOURNAL.PONE.0008570

(-) Compounds

Molecule 1 - EUCHROMATIC HISTONE METHYLTRANSFERASE 1
    ChainsA, B
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentC-TERMINAL DOMAIN, RESIDUES 951-1235
    GeneEHMT1, EUHMTASE1, KIAA1876
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymEHMT1, HISTONE H3-K9 METHYLTRANSFERASE 5, H3-K9- HMTASE 5, EUCHROMATIC HISTONE-LYSINE, HISTONE-LYSINE N- METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 5 N- METHYLTRANSFERASE 1, EU-HMTASE1, G9A- LIKE PROTEIN 1, GLP1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2ZN8Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:1031 , CYS A:1044 , CYS A:1074 , CYS A:1078BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWARECYS A:1037 , CYS A:1074 , CYS A:1080 , CYS A:1084BINDING SITE FOR RESIDUE ZN A 502
03AC3SOFTWARECYS A:1031 , CYS A:1033 , CYS A:1037 , CYS A:1042BINDING SITE FOR RESIDUE ZN A 503
04AC4SOFTWARECYS A:1172 , CYS A:1225 , CYS A:1227 , CYS A:1232BINDING SITE FOR RESIDUE ZN A 504
05AC5SOFTWARECYS B:1031 , CYS B:1044 , CYS B:1074 , CYS B:1078BINDING SITE FOR RESIDUE ZN B 501
06AC6SOFTWARECYS B:1037 , CYS B:1074 , CYS B:1080 , CYS B:1084BINDING SITE FOR RESIDUE ZN B 502
07AC7SOFTWARECYS B:1031 , CYS B:1033 , CYS B:1037 , CYS B:1042BINDING SITE FOR RESIDUE ZN B 503
08AC8SOFTWARECYS B:1172 , CYS B:1225 , CYS B:1227 , CYS B:1232BINDING SITE FOR RESIDUE ZN B 504
09AC9SOFTWAREMET A:1105 , TRP A:1107 , SER A:1141 , TYR A:1142 , ARG A:1166 , PHE A:1167 , ILE A:1168 , ASN A:1169 , HIS A:1170 , TYR A:1211 , PHE A:1215 , CYS A:1225 , ARG A:1226 , HOH A:1336BINDING SITE FOR RESIDUE SAH A 101
10BC1SOFTWAREMET B:1105 , GLY B:1106 , TRP B:1107 , SER B:1141 , TYR B:1142 , ARG B:1166 , PHE B:1167 , ASN B:1169 , HIS B:1170 , TYR B:1211 , PHE B:1215 , CYS B:1225 , ARG B:1226 , HOH B:1324 , HOH B:1341 , HOH B:1412 , HOH B:1465 , HOH B:1523BINDING SITE FOR RESIDUE SAH B 102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069183C1075YEHMT1_HUMANDisease (KLESTS)  ---A/BC1044Y
2UniProtVAR_036346Y1173FEHMT1_HUMANUnclassified  ---A/BY1142F

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PRE_SETPS50867 Pre-SET domain profile.EHMT1_HUMAN1060-1123
 
  2A:1029-1092
B:1029-1092
2SETPS50280 SET domain profile.EHMT1_HUMAN1126-1243
 
  2A:1095-1212
B:1095-1212

(-) Exons   (0, 0)

(no "Exon" information available for 2IGQ)

(-) 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:251
 aligned with EHMT1_HUMAN | Q9H9B1 from UniProtKB/Swiss-Prot  Length:1298

    Alignment length:260
                                  1016      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266
         EHMT1_HUMAN   1007 ERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRCGSPKCRHS 1266
               SCOP domains d2igqa_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.............eee...........ee....ee........hhhhh.............hhhhhhh......................ee...............hhhhh....eeeee.....eeeee........eeee..eeeeehhhhhh......eee.------.eeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh---............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------Y-------------------------------------------------------------------------------------------------F--------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------PRE_SET  PDB: A:1029-1092 UniProt: 1060-1123                    --SET  PDB: A:1095-1212 UniProt: 1126-1243                                                                              ----------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2igq A  976 ERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDL------VYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKG---SCRCGSPKCRHS 1235
                                   985       995      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145|     1155      1165      1175      1185      1195      1205      1215    | 1225      1235
                                                                                                                                                                                                   1146   1153                                                               1220   |           
                                                                                                                                                                                                                                                                                 1224           

Chain B from PDB  Type:PROTEIN  Length:254
 aligned with EHMT1_HUMAN | Q9H9B1 from UniProtKB/Swiss-Prot  Length:1298

    Alignment length:260
                                  1016      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266
         EHMT1_HUMAN   1007 ERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRCGSPKCRHS 1266
               SCOP domains d2igqb_ B: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.............eee...........ee..............hhhhh.............hhhhhhh......................ee...............hhhhh....eeee.......eeee........eeee...eeeehhhhhh......eee..----..eeee...eehhhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhh--.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------Y-------------------------------------------------------------------------------------------------F--------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------PRE_SET  PDB: B:1029-1092 UniProt: 1060-1123                    --SET  PDB: B:1095-1212 UniProt: 1126-1243                                                                              ----------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2igq B  976 ERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLD----EVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIK--LFSCRCGSPKCRHS 1235
                                   985       995      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145 |    1155      1165      1175      1185      1195      1205      1215   |  1225      1235
                                                                                                                                                                                                    1147 1152                                                               1219  |             
                                                                                                                                                                                                                                                                               1222             

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (EHMT1_HUMAN | Q9H9B1)
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: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:0046974    histone methyltransferase activity (H3-K9 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 9) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 9). This reaction is the addition of a methyl group onto lysine at position 9 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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    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:0009790    embryo development    The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
    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:0051567    histone H3-K9 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 9 of the histone.
    GO:0034968    histone lysine methylation    The modification of a histone by addition of one or more methyl groups to a lysine residue.
    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: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:0018027    peptidyl-lysine dimethylation    The methylation of peptidyl-lysine to form peptidyl-N6,N6-dimethyl-L-lysine.
    GO:0018026    peptidyl-lysine monomethylation    The methylation of peptidyl-lysine to form peptidyl-N6-methyl-L-lysine.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0060992    response to fungicide    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 a fungicide stimulus. Fungicides are chemicals used to kill fungi.
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: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
        EHMT1_HUMAN | Q9H9B12rfi 3b7b 3b95 3fpd 3hna 3mo0 3mo2 3mo5 3sw9 3swc 4i51 5ttg 5tuz 5vsd 5vsf

(-) Related Entries Specified in the PDB File

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