CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-021468
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Histone-lysine N-methyltransferase SMYD3 
Protein Synonyms/Alias
 SET and MYND domain-containing protein 3; Zinc finger MYND domain-containing protein 1 
Gene Name
 SMYD3 
Gene Synonyms/Alias
 ZMYND1; ZNFN3A1 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
5***MEPLKVEKFATAubiquitination[1]
42PLAYTVCKGSRGVVCubiquitination[1]
122GAPSESEKLYSFYDLubiquitination[2]
141NKLTEDKKEGLRQLVubiquitination[1]
375VRGVQVMKVGKLQLHubiquitination[1]
378VQVMKVGKLQLHQGMubiquitination[1, 3, 4, 5]
391GMFPQAMKNLRLAFDubiquitination[1, 3, 4, 5]
Reference
 [1] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [2] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [3] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [4] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
 [5] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302] 
Functional Description
 Histone methyltransferase. Specifically methylates 'Lys- 4' and 'Lys-5' of histone H3, inducing di- and tri-methylation, but not monomethylation. Plays an important role in transcriptional activation as a member of an RNA polymerase complex. Binds DNA containing 5'-CCCTCC-3' or 5'-GAGGGG-3' sequences. 
Sequence Annotation
 DOMAIN 4 240 SET.
 ZN_FING 49 87 MYND-type.
 REGION 14 16 S-adenosyl-L-methionine binding.
 REGION 205 206 S-adenosyl-L-methionine binding.
 BINDING 124 124 S-adenosyl-L-methionine.
 BINDING 132 132 S-adenosyl-L-methionine.
 BINDING 181 181 S-adenosyl-L-methionine.
 BINDING 239 239 S-adenosyl-L-methionine.
 BINDING 259 259 S-adenosyl-L-methionine.  
Keyword
 3D-structure; Alternative splicing; Chromatin regulator; Complete proteome; Cytoplasm; Metal-binding; Methyltransferase; Nucleus; Reference proteome; S-adenosyl-L-methionine; Transferase; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 428 AA 
Protein Sequence
MEPLKVEKFA TAKRGNGLRA VTPLRPGELL FRSDPLAYTV CKGSRGVVCD RCLLGKEKLM 60
RCSQCRVAKY CSAKCQKKAW PDHKRECKCL KSCKPRYPPD SVRLLGRVVF KLMDGAPSES 120
EKLYSFYDLE SNINKLTEDK KEGLRQLVMT FQHFMREEIQ DASQLPPAFD LFEAFAKVIC 180
NSFTICNAEM QEVGVGLYPS ISLLNHSCDP NCSIVFNGPH LLLRAVRDIE VGEELTICYL 240
DMLMTSEERR KQLRDQYCFE CDCFRCQTQD KDADMLTGDE QVWKEVQESL KKIEELKAHW 300
KWEQVLAMCQ AIISSNSERL PDINIYQLKV LDCAMDACIN LGLLEEALFY GTRTMEPYRI 360
FFPGSHPVRG VQVMKVGKLQ LHQGMFPQAM KNLRLAFDIM RVTHGREHSL IEDLILLLEE 420
CDANIRAS 428 
Gene Ontology
 GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
 GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
 GO:0018024; F:histone-lysine N-methyltransferase activity; ISS:UniProtKB.
 GO:0008270; F:zinc ion binding; IEA:InterPro. 
Interpro
 IPR025805; Hist-Lys_N-MeTrfase_Smyd3.
 IPR001214; SET_dom.
 IPR002893; Znf_MYND. 
Pfam
 PF00856; SET
 PF01753; zf-MYND 
SMART
 SM00317; SET 
PROSITE
 PS51574; SAM_MT43_2
 PS50280; SET
 PS01360; ZF_MYND_1
 PS50865; ZF_MYND_2 
PRINTS