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(-) Description

Title :  CRYSTAL STRUCTURE OF CARDIAC SPECIFIC HISTONE METHYLTRANSFERASE SMYD1
 
Authors :  N. Sirinupong, Z. Yang
Date :  26 May 10  (Deposition) - 13 Oct 10  (Release) - 05 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Histone Lysine Methyltransferase, Smyd1, Heart Development, Mynd, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Sirinupong, J. Brunzelle, J. Ye, A. Pirzada, L. Nico, Z. Yang
Crystal Structure Of Cardiac-Specific Histone Methyltransferase Smyd1 Reveals Unusual Active Site Architecture.
J. Biol. Chem. V. 285 40635 2010
PubMed-ID: 20943667  |  Reference-DOI: 10.1074/JBC.M110.168187

(-) Compounds

Molecule 1 - HISTONE LYSINE METHYLTRANSFERASE SMYD1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSUMO
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneMCG_127279, SMYD1
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymSET AND MYND DOMAIN CONTAINING 1, ISOFORM CRA_B, SMYD1 PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SFG1Ligand/IonADENOSYL-ORNITHINE
4ZN3Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:17 , ARG A:19 , GLN A:133 , HIS A:135 , ASN A:180 , GLY A:202 , LEU A:203 , VAL A:204 , ASN A:205 , HIS A:206 , TYR A:252 , TYR A:270 , PHE A:272BINDING SITE FOR RESIDUE SFG A 491
2AC2SOFTWAREVAL A:114 , ASP A:130 , PHE A:165 , SER A:166 , TYR A:169BINDING SITE FOR RESIDUE MES A 492
3AC3SOFTWAREPHE A:44 , ASP A:45 , SER A:46 , GLU A:102BINDING SITE FOR RESIDUE GOL A 493
4AC4SOFTWARELEU A:47 , ARG A:58 , GLN A:191BINDING SITE FOR RESIDUE GOL A 494
5AC5SOFTWARECYS A:52 , CYS A:55 , CYS A:74 , CYS A:78BINDING SITE FOR RESIDUE ZN A 495
6AC6SOFTWARECYS A:65 , CYS A:68 , HIS A:86 , CYS A:90BINDING SITE FOR RESIDUE ZN A 496
7AC7SOFTWARECYS A:208 , CYS A:274 , CYS A:276 , CYS A:279BINDING SITE FOR RESIDUE ZN A 497

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N71)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3N71)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SMYD1_MOUSE_001 *K95RSMYD1_MOUSE  ---  ---AK95R
2UniProtVAR_SMYD1_MOUSE_002 *P160LSMYD1_MOUSE  ---  ---AP160L
3UniProtVAR_SMYD1_MOUSE_003 *A344TSMYD1_MOUSE  ---  ---AA344T
   * ID not provided by source

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

(-) PROSITE Motifs  (3, 2)

Asymmetric/Biological Unit (3, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.SMYD1_MOUSE7-253  1A:7-253
2ZF_MYND_1PS01360 Zinc finger MYND-type signature.SMYD1_MOUSE52-90  1A:52-90
3ZF_MYND_2PS50865 Zinc finger MYND-type profile.SMYD1_MOUSE52-90  1A:52-90

(-) Exons   (0, 0)

(no "Exon" information available for 3N71)

(-) 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:468
 aligned with SMYD1_MOUSE | P97443 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:468
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460        
          SMYD1_MOUSE     1 MTIGSMENVEVFTSEGKGRGLKATKEFWAADVIFAERAYSAVVFDSLINFVCHTCFKRQEKLHRCGQCKFAHYCDRTCQKDAWLNHKNECAAIKKYGKVPNENIRLAARIMWRVEREGTGLTEGCLVSVDDLQNHVEHFGEEEQKELRVDVDTFLQYWPPQSQQFSMQYISHIFGVINCNGFTLSDQRGLQAVGVGIFPNLGLVNHDCWPNCTVIFNNGNHEAVKSMFHTQMRIELRALGKISEGEELTVSYIDFLHLSEERRRQLKKQYYFDCSCEHCQKGLKDDLFLAAKEDPKPSQEVVKEMIQFSKDTLEKIDKARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREAALNN 468
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeee.....eeeee........eeeee...eeee.hhhh..............ee.......ee.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.eeeee......eeeeee..hhhhhee.....eeeeee.........hhhhh.eeeeee..........ee.......hhhhhhhhhhhhhh....hhhhhhh.hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------R----------------------------------------------------------------L---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------SET  PDB: A:7-253 UniProt: 7-253                                                                                                                                                                                                                       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------ZF_MYND_2  PDB: A:52-90 UniProt: 52-90 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) ---------------------------------------------------ZF_MYND_1  PDB: A:52-90 UniProt: 52-90 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3n71 A   1 MTIGSMENVEVFTSEGKGRGLKATKEFWAADVIFAERAYSAVVFDSLINFVCHTCFKRQEKLHRCGQCKFAHYCDRTCQKDAWLNHKNECAAIKKYGKVPNENIRLAARIMWRVEREGTGLTEGCLVSVDDLQNHVEHFGEEEQKELRVDVDTFLQYWPPQSQQFSMQYISHIFGVINCNGFTLSDQRGLQAVGVGIFPNLGLVNHDCWPNCTVIFNNGNHEAVKSMFHTQMRIELRALGKISEGEELTVSYIDFLHLSEERRRQLKKQYYFDCSCEHCQKGLKDDLFLAAKEDPKPSQEVVKEMIQFSKDTLEKIDKARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREAALNN 468
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460        

   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 3N71)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N71)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3N71)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SMYD1_MOUSE | P97443)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    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: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:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    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: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:0045663    positive regulation of myoblast differentiation    Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
    GO:0010831    positive regulation of myotube differentiation    Any process that activates, maintains or increases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0035914    skeletal muscle cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle cell, a somatic cell located in skeletal muscle.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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