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(-) Description

Title :  CRYSTAL STRUCTURE OF SMYD3 IN COMPLEX WITH METHYLTRANSFERASE INHIBITOR SINEFUNGIN
 
Authors :  N. Sirinupong, J. Brunzelle, Z. Yang
Date :  23 Oct 10  (Deposition) - 17 Nov 10  (Release) - 09 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann Fold, Zinc Finger, Methyltransferase, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Sirinupong, J. Brunzelle, E. Doko, Z. Yang
Structural Insights Into The Autoinhibition And Posttranslational Activation Of Histone Methyltransferase Smyd3.
J. Mol. Biol. V. 406 149 2011
PubMed-ID: 21167177  |  Reference-DOI: 10.1016/J.JMB.2010.12.014

(-) Compounds

Molecule 1 - SET AND MYND DOMAIN-CONTAINING PROTEIN 3
    ChainsA
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneSMYD3, ZMYND1, ZNFN3A1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymZINC FINGER MYND DOMAIN-CONTAINING PROTEIN 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2MG2Ligand/IonMAGNESIUM ION
3SFG1Ligand/IonADENOSYL-ORNITHINE
4ZN3Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:14 , ASN A:16 , TYR A:124 , GLU A:130 , ASN A:132 , CYS A:180 , ASN A:181 , SER A:202 , LEU A:203 , LEU A:204 , ASN A:205 , HIS A:206 , TYR A:239 , TYR A:257 , PHE A:259 , GOL A:431 , HOH A:655 , HOH A:670 , HOH A:674 , HOH A:697 , HOH A:725 , HOH A:766 , HOH A:827BINDING SITE FOR RESIDUE SFG A 429
02AC2SOFTWARECYS A:238 , LEU A:240 , MET A:242 , HIS A:366 , GOL A:432 , HOH A:669 , HOH A:678 , HOH A:837BINDING SITE FOR RESIDUE GOL A 430
03AC3SOFTWAREASN A:181 , SER A:182 , PHE A:183 , SER A:202 , ILE A:237 , TYR A:239 , TYR A:257 , SFG A:429 , HOH A:702 , HOH A:938BINDING SITE FOR RESIDUE GOL A 431
04AC4SOFTWAREILE A:214 , VAL A:215 , HIS A:366 , PRO A:367 , VAL A:368 , GOL A:430 , HOH A:652 , HOH A:693 , HOH A:779BINDING SITE FOR RESIDUE GOL A 432
05AC5SOFTWAREPRO A:81 , ASP A:82 , LYS A:111 , GLY A:115 , GLU A:142 , GLN A:146 , HOH A:536 , HOH A:738 , HOH A:1015BINDING SITE FOR RESIDUE GOL A 433
06AC6SOFTWAREPHE A:151 , GLN A:152 , ILE A:159 , LEU A:171 , HOH A:602 , HOH A:817BINDING SITE FOR RESIDUE GOL A 434
07AC7SOFTWAREPHE A:126 , ALA A:168 , PHE A:169 , ASP A:170 , GLU A:173 , ALA A:174 , LYS A:177 , HOH A:461 , HOH A:528 , HOH A:853 , HOH A:1036BINDING SITE FOR RESIDUE GOL A 435
08AC8SOFTWARECYS A:62 , CYS A:65 , HIS A:83 , CYS A:87BINDING SITE FOR RESIDUE ZN A 436
09AC9SOFTWARECYS A:49 , CYS A:52 , CYS A:71 , CYS A:75BINDING SITE FOR RESIDUE ZN A 437
10BC1SOFTWARECYS A:208 , CYS A:261 , CYS A:263 , CYS A:266BINDING SITE FOR RESIDUE ZN A 438
11BC2SOFTWAREHOH A:751 , HOH A:791 , HOH A:875 , HOH A:932 , HOH A:1002 , HOH A:1003BINDING SITE FOR RESIDUE MG A 439
12BC3SOFTWAREHOH A:869 , HOH A:896 , HOH A:1004 , HOH A:1005 , HOH A:1006BINDING SITE FOR RESIDUE MG A 440

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:94 -Pro A:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PDN)

(-) PROSITE Motifs  (3, 2)

Asymmetric/Biological Unit (3, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.SMYD3_HUMAN4-240  1A:4-240
2ZF_MYND_1PS01360 Zinc finger MYND-type signature.SMYD3_HUMAN49-87  1A:49-87
3ZF_MYND_2PS50865 Zinc finger MYND-type profile.SMYD3_HUMAN49-87  1A:49-87

(-) Exons   (0, 0)

(no "Exon" information available for 3PDN)

(-) 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 SMYD3_HUMAN | Q9H7B4 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:427
                                    11        21        31        41        51        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       351       361       371       381       391       401       411       421       
          SMYD3_HUMAN     2 EPLKVEKFATAKRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRAS 428
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------zf-MYND-3pdnA01 A:49-87                ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------SET-3pdnA02 A:15-240                                                                                                                                                                                                              -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eeeee.....eeeee........eeeee...eeee...................ee.......ee.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh....hhhhhhhhhhhhheeee.....eeeeee..hhhhhee.....eeeeee..eeeeee........eeee.......hhhhhhhhhhhhhh....hhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --SET  PDB: A:4-240 UniProt: 4-240                                                                                                                                                                                                             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------ZF_MYND_2  PDB: A:49-87 UniProt: 49-87 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------ZF_MYND_1  PDB: A:49-87 UniProt: 49-87 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pdn A   2 EPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRAS 428
                                    11        21        31        41        51        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       351       361       371       381       391       401       411       421       

   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 3PDN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: TRASH (61)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SMYD3_HUMAN | Q9H7B4)
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:0000979    RNA polymerase II core promoter sequence-specific DNA binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery.
    GO:0001162    RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with an RNA polymerase II intronic DNA sequence that regulates the transcription of the transcript it is contained within.
    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: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:0071549    cellular response to dexamethasone 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 dexamethasone stimulus.
    GO:0045184    establishment of protein localization    The directed movement of a protein to a specific location.
    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:0014904    myotube cell development    The process aimed at the progression of a myotube cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0033138    positive regulation of peptidyl-serine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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
        SMYD3_HUMAN | Q9H7B43mek 3oxf 3oxg 3oxl 3qwp 3ru0 5ccl 5ccm 5ex0 5ex3 5hi7 5hq8

(-) Related Entries Specified in the PDB File

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