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(-) Description

Title :  METHYLTRANSFERASE DOMAIN OF HUMAN SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 2
 
Authors :  V. V. Lunin, H. Wu, H. Zeng, H. Ren, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, J. Min, Structural Genomics Consortium (Sgc)
Date :  29 Aug 07  (Deposition) - 11 Sep 07  (Release) - 02 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Histone H3-K9 Methyltransferase 2, Histone-Lysine N- Methyltransferase, H3 Lysine-9 Specific 2, Alternative Splicing, Cell Cycle, Chromatin Regulator, Chromosomal Protein, Differentiation, Nucleus, Repressor, S-Adenosyl-L- Methionine, Telomere, Transcription, Transcription Regulation, 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 - HISTONE-LYSINE N-METHYLTRANSFERASE SUV39H2
    ChainsA
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP15MHL
    Expression System StrainDH5A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentMETHYLTRANSFERASE DOMAIN: RESIDUES 112-410
    GeneSUV39H2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 2, SU(VAR)3- 9 HOMOLOG 2, HISTONE H3-K9 METHYLTRANSFERASE 2, H3-K9- HMTASE 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
2SER1Mod. Amino AcidSERINE
3ZN4Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:222 , CYS A:287 , CYS A:289 , CYS A:294BINDING SITE FOR RESIDUE ZN A 300
2AC2SOFTWARECYS A:80 , CYS A:82 , CYS A:85 , CYS A:90BINDING SITE FOR RESIDUE ZN A 301
3AC3SOFTWARECYS A:80 , CYS A:91 , CYS A:118 , CYS A:122BINDING SITE FOR RESIDUE ZN A 302
4AC4SOFTWARECYS A:85 , CYS A:118 , CYS A:124 , CYS A:128BINDING SITE FOR RESIDUE ZN A 303
5AC5SOFTWAREARG A:150 , GLY A:151 , TRP A:152 , LYS A:189 , THR A:192 , TYR A:193 , HIS A:216 , PHE A:217 , VAL A:218 , ASN A:219 , HIS A:220 , TYR A:261 , VAL A:286 , CYS A:287 , LYS A:288 , CYS A:289 , LEU A:298 , HOH A:324 , HOH A:415 , HOH A:486 , HOH A:488 , HOH A:490BINDING SITE FOR RESIDUE SAM A 304
6AC6SOFTWARETHR A:83 , ASP A:84 , CYS A:85 , GLY A:125 , CYS A:128 , HOH A:554 , HOH A:557BINDING SITE FOR RESIDUE SER A 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R3A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R3A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R3A)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PRE_SETPS50867 Pre-SET domain profile.SUV92_HUMAN189-247  1A:78-136
2SETPS50280 SET domain profile.SUV92_HUMAN250-373  1A:139-262
3POST_SETPS50868 Post-SET domain profile.SUV92_HUMAN394-410  1A:283-299

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1dENST000003549191dENSE00001932261chr10:14920888-1492091831SUV92_HUMAN1-11110--
1.3ENST000003549193ENSE00001720133chr10:14923499-14923644146SUV92_HUMAN11-59490--
1.4dENST000003549194dENSE00001692038chr10:14938845-14939516672SUV92_HUMAN60-2832241A:13-172 (gaps)160
1.5ENST000003549195ENSE00001098457chr10:14941538-14941684147SUV92_HUMAN284-332491A:173-22149
1.6ENST000003549196ENSE00001098462chr10:14943132-14943261130SUV92_HUMAN333-376441A:222-26544
1.7bENST000003549197bENSE00001815292chr10:14944405-14944511107SUV92_HUMAN376-410351A:265-299 (gaps)35

(-) 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:271
 aligned with SUV92_HUMAN | Q9H5I1 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:288
                                                                                                                                                                                                                                                                                                                        410 
                                   133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403      | 
          SUV92_HUMAN   124 AEYIVKKAKQRIALQRWQDELNRRKNHKGMIFVENTVDLEGPPSDFYYINEYKPAPGISLVNEATFGCSCTDCFFQKCCPAEAGVLLAYNKNQQIKIPPGTPIYECNSRCQCGPDCPNRIVQKGTQYSLCIFRTSNGRGWGVKTLVKIKRMSFVMEYVGEVITSEEAERRGQFYDNKGITYLFDLDYESDEFTVDAARYGNVSHFVNHSCDPNLQVFNVFIDNLDTRLPRIALFSTRTINAGEELTFDYQMKGSGDISSDSIDHSPAKKRVRTVCKCGAVTCRGYLN-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------Pre-SET-2r3aA01 A:33-131                                                                           -------------------SET-2r3aA02 A:151-262                                                                                           -----              ------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.....eeee............ee....ee.......---.............hhhhhh...................ee...............hhhhh....eeeee......eeeee........eeeee..eeeehhhhhhhhhh.hhhhhhheee.......eeee...eehhhhhhee.....eeeeeee.........eeeeee........eeeehhhhh...--------------................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------PRE_SET  PDB: A:78-136 UniProt: 189-247                    --SET  PDB: A:139-262 UniProt: 250-373                                                                                        --------------------POST_SET         - PROSITE
           Transcript 1 (1) Exon 1.4d  PDB: A:13-172 (gaps) UniProt: 60-283 [INCOMPLETE]                                                                                                    Exon 1.5  PDB: A:173-221 UniProt: 284-332        Exon 1.6  PDB: A:222-265 UniProt: 333-376   ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7b  PDB: A:265-299 (gaps)   - Transcript 1 (2)
                 2r3a A  13 AEYIVKKAKQRIALQRWQDELNRRKNHKGMIFVENTVDLEGPPSDFYYINEYKPAPGISLV---TFGCSCTDCFFQKCCPAEAGVLLAYNKNQQIKIPPGTPIYECNSRCQCGPDCPNRIVQKGTQYSLCIFRTSNGRGWGVKTLVKIKRMSFVMEYVGEVITSEEAERRGQFYDNKGITYLFDLDYESDEFTVDAARYGNVSHFVNHSCDPNLQVFNVFIDNLDTRLPRIALFSTRTINAGEELTFDYQMKGSG--------------RVRTVCKCGAVTCRGYLNS 305
                                    22        32        42        52        62        72|   |   82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262    |    -       282       292      ||
                                                                                       73  77                                                                                                                                                                                           267            282              299|
                                                                                                                                                                                                                                                                                                                         305

   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 2R3A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2R3A)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Family: SET (46)

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SUV92_HUMAN | Q9H5I1)
molecular function
    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: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:0000976    transcription regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
    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:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0071456    cellular response to hypoxia    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 lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0006333    chromatin assembly or disassembly    The formation or destruction of chromatin structures.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0036123    histone H3-K9 dimethylation    The modification of histone H3 by addition of two methyl groups to lysine at position 9 of the histone.
    GO:0036124    histone H3-K9 trimethylation    The modification of histone H3 by addition of three 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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0042754    negative regulation of circadian rhythm    Any process that stops, prevents, or reduces the frequency, rate or extent of a circadian rhythm behavior.
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    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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