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(-) Description

Title :  STRUCTURE OF SMYD2 IN COMPLEX WITH SAM
 
Authors :  K. Zhao, L. Wang
Date :  17 Aug 11  (Deposition) - 31 Aug 11  (Release) - 14 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Set Domain, Methyltransferase, Co Factor Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Wang, L. Li, H. Zhang, X. Luo, J. Dai, S. Zhou, J. Gu, J. Zhu, P. Atadja, C. Lu, E. Li, K. Zhao
Structure Of Human Smyd2 Reveals The Basis Of P53 Tumor Suppressor Methylation
J. Biol. Chem. 2011
PubMed-ID: 21880715  |  Reference-DOI: 10.1074/JBC.M111.262410

(-) Compounds

Molecule 1 - N-LYSINE METHYLTRANSFERASE SMYD2
    ChainsA
    EC Number2.1.1.-, 2.1.1.43
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System PlasmidPFASTBAC
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    GeneSMYD2, KMT3C
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHSKM-B, HISTONE METHYLTRANSFERASE SMYD2, LYSINE N- METHYLTRANSFERASE 3C, SET AND MYND DOMAIN-CONTAINING PROTEIN 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
3ZN3Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:16 , LYS A:17 , ARG A:19 , HIS A:137 , CYS A:181 , ASN A:182 , ALA A:203 , LEU A:204 , ASN A:206 , HIS A:207 , TYR A:240 , TYR A:258 , PHE A:260 , GOL A:438 , HOH A:597 , HOH A:609 , HOH A:625 , HOH A:639BINDING SITE FOR RESIDUE SAM A 434
2AC2SOFTWARECYS A:52 , CYS A:55 , CYS A:74 , CYS A:78BINDING SITE FOR RESIDUE ZN A 435
3AC3SOFTWARECYS A:65 , CYS A:68 , HIS A:86 , CYS A:90BINDING SITE FOR RESIDUE ZN A 436
4AC4SOFTWARECYS A:209 , CYS A:262 , CYS A:264 , CYS A:267BINDING SITE FOR RESIDUE ZN A 437
5AC5SOFTWARECYS A:181 , ASN A:182 , GLY A:183 , PHE A:184 , ALA A:203 , TYR A:240 , TYR A:258 , SAM A:434 , GOL A:439 , HOH A:463BINDING SITE FOR RESIDUE GOL A 438
6AC6SOFTWAREPHE A:184 , THR A:185 , TYR A:240 , GOL A:438 , HOH A:535 , HOH A:561BINDING SITE FOR RESIDUE GOL A 439
7AC7SOFTWARECYS A:209 , LEU A:243 , ARG A:250 , GLU A:266 , LYS A:272 , LYS A:276 , HIS A:373 , TYR A:374 , PRO A:375BINDING SITE FOR RESIDUE GOL A 440
8AC8SOFTWAREGLU A:190 , ARG A:390 , LEU A:391 , HOH A:617BINDING SITE FOR RESIDUE GOL A 441
9AC9SOFTWAREALA A:38 , TYR A:39 , LYS A:115 , HOH A:596 , HOH A:624 , HOH A:648BINDING SITE FOR RESIDUE GOL A 442

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TG4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TG4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_023442G165ESMYD2_HUMANPolymorphism1134647AG165E
2UniProtVAR_052991I430MSMYD2_HUMANPolymorphism11120301AI430M

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.SMYD2_HUMAN7-241  1A:7-241
2ZF_MYND_1PS01360 Zinc finger MYND-type signature.SMYD2_HUMAN51-90  1A:51-90
3ZF_MYND_2PS50865 Zinc finger MYND-type profile.SMYD2_HUMAN52-90  1A:52-90

(-) Exons   (0, 0)

(no "Exon" information available for 3TG4)

(-) 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:427
 aligned with SMYD2_HUMAN | Q9NRG4 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:427
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       
          SMYD2_HUMAN     6 LGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLGFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIES 432
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....eeeee........eeeeee..eeee.hhhh..............ee.......ee.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhheeee.....eeeeeehhhhhh.ee.....eeeeee..eeeeee..........ee.......hhhhhhhhhhhhhh....hhhhhhh.hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------E------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------M-- SAPs(SNPs)
                PROSITE (1) -SET  PDB: A:7-241 UniProt: 7-241                                                                                                                                                                                                           ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------ZF_MYND_1  PDB: A:51-90 UniProt: 51-90  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) ----------------------------------------------ZF_MYND_2  PDB: A:52-90 UniProt: 52-90 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tg4 A   6 LGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLGFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIES 432
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       

   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 3TG4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TG4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TG4)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SMYD2_HUMAN | Q9NRG4)
molecular function
    GO:0000993    RNA polymerase II core binding    Interacting selectively and non-covalently with RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits.
    GO:0046975    histone methyltransferase activity (H3-K36 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 36) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 36). This reaction is the addition of a methyl group onto lysine at position 36 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:0016278    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.
    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.
biological process
    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:0010452    histone H3-K36 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 36 of the histone.
    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:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    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: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:0043516    regulation of DNA damage response, signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of the cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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
        SMYD2_HUMAN | Q9NRG43rib 3s7b 3s7d 3s7f 3s7j 3tg5 4o6f 4wuy 4ynd 5arf 5arg 5kjk 5kjl 5kjm 5kjn

(-) Related Entries Specified in the PDB File

3tg5