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Title :   CRYSTAL STRUCTURE OF HUMAN HISTONE-LYSINE N-METHYLTRANSFERASE SMYD3 IN COMPLEX WITH S-ADENOSYL-L-METHIONINE

Authors :   R. Lam, L. Dombrovski, Y. Li, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, J. Min, H. Wu, Structural Genomics Consortium (Sgc)

Date :   31 Mar 10 (Deposition) - 14 Apr 10 (Release) - 14 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A

Keywords :   Histone Methyltransferase, Set And Mynd Domain-Containing Protein 3, Zinc Finger Mynd Domain-Containing Protein 1, Histone H3, Di-Methylation, Tri-Methylation, Transcriptional Activation, Dna-Binding, Mynd-Type Zinc Finger, Set Domain, Chromatin Modification, Alternative Splicing, Chromatin Regulator, Cytoplasm, Metal-Binding, Methyltransferase, Nucleus, S-Adenosyl-L-Methionine, Transferase, Zinc, Zinc-Finger, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Lam, L. Dombrovski, Y. Li, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, J. Min, H. Wu
Crystal Structure Of Human Histone-Lysine N-Methyltransferase Smyd3 In Complex With S-Adenosyl-L-Methionine
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 19)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 2)

Exons (0, 0)

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:423
 aligned with SMYD3_HUMAN | Q9H7B4 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:423
                                    12        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       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422   
          SMYD3_HUMAN     3 PLKVEKFATAKRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANI 425
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....eeeee........eeeee...eeee...................ee.......ee.hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh....hhhhhhhhhhhhheeee.....eeeeee..hhhhhee.....eeeeee..eeeeee........eeee.......hhhhhhhhhhhhhh....hhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -SET  PDB: A:4-240 UniProt: 4-240                                                                                                                                                                                                             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------ZF_MYND_1  PDB: A:49-87 UniProt: 49-87 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------------------------------------ZF_MYND_2  PDB: A:49-87 UniProt: 49-87 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mek A   3 PLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLmRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLmDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVmTFQHFmREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEmQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDmLmTSEERRKQLRDQYCFECDCFRCQTQDKDADmLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAmCQAIISSNSERLPDINIYQLKVLDCAmDACINLGLLEEALFYGTRTmEPYRIFFPGSHPVRGVQVmKVGKLQLHQGmFPQAmKNLRLAFDImRVTHGREHSLIEDLILLLEECDANI 425
                                    12        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       272  |    282       292       302     | 312       322       332  |    342       352  |    362       372 |     382  |    392       402       412       422   
                                                                                    60-MSE                                              113-MSE                             149-MSE |                                190-MSE                                             242-MSE                          275-MSE                          308-MSE                    335-MSE             355-MSE            374-MSE    385-MSE|       400-MSE                     
                                                                                                                                                                                  155-MSE                                                                                  244-MSE                                                                                                                                           390-MSE

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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

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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	SMYD3_HUMAN \| Q9H7B4
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	2.1.1.43
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