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Protein

Histone-lysine N-methyltransferase SMYD3

Gene

Smyd3

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

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 (By similarity).By similarity

Catalytic activityi

S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].PROSITE-ProRule annotation

Enzyme regulationi

Histone methyltransferase activity strongly stimulated by HSPCA.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei124 – 1241S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei132 – 1321S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei239 – 2391S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei259 – 2591S-adenosyl-L-methioninePROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri49 – 8739MYND-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • histone-lysine N-methyltransferase activity Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW
  • RNA polymerase II core binding Source: MGI
  • RNA polymerase II core promoter sequence-specific DNA binding Source: MGI
  • RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding Source: MGI

GO - Biological processi

  • cellular response to dexamethasone stimulus Source: MGI
  • establishment of protein localization Source: MGI
  • myotube cell development Source: MGI
  • negative regulation of protein kinase activity Source: MGI
  • nucleosome assembly Source: MGI
  • positive regulation of peptidyl-serine phosphorylation Source: MGI
  • positive regulation of transcription from RNA polymerase II promoter Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Methyltransferase, Transferase

Keywords - Ligandi

Metal-binding, S-adenosyl-L-methionine, Zinc

Enzyme and pathway databases

BRENDAi2.1.1.43. 3474.
ReactomeiREACT_278269. PKMTs methylate histone lysines.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone-lysine N-methyltransferase SMYD3 (EC:2.1.1.43)
Alternative name(s):
SET and MYND domain-containing protein 3
Zinc finger MYND domain-containing protein 1
Gene namesi
Name:Smyd3
Synonyms:Zmynd1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 1

Organism-specific databases

MGIiMGI:1916976. Smyd3.

Subcellular locationi

  • Cytoplasm By similarity
  • Nucleus By similarity

  • Note: Mainly cytoplasmic when cells are arrested at G0/G1. Accumulates in the nucleus at S phase and G2/M.By similarity

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 428428Histone-lysine N-methyltransferase SMYD3PRO_0000218313Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineBy similarity

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiQ9CWR2.
PaxDbiQ9CWR2.
PRIDEiQ9CWR2.

PTM databases

PhosphoSiteiQ9CWR2.

Expressioni

Gene expression databases

BgeeiQ9CWR2.
CleanExiMM_SMYD3.
ExpressionAtlasiQ9CWR2. baseline and differential.
GenevisibleiQ9CWR2. MM.

Interactioni

Subunit structurei

Interacts with HSPCA. Interacts with HELZ. Interacts with POLR2A; the interaction may be indirect and may be mediated by HELZ (By similarity).By similarity

Protein-protein interaction databases

BioGridi213640. 1 interaction.
STRINGi10090.ENSMUSP00000117410.

Structurei

3D structure databases

ProteinModelPortaliQ9CWR2.
SMRiQ9CWR2. Positions 4-428.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini4 – 240237SETPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni14 – 163S-adenosyl-L-methionine bindingBy similarity
Regioni205 – 2062S-adenosyl-L-methionine bindingBy similarity

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family.PROSITE-ProRule annotation
Contains 1 MYND-type zinc finger.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri49 – 8739MYND-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG2940.
GeneTreeiENSGT00530000063077.
HOGENOMiHOG000007850.
HOVERGENiHBG105004.
InParanoidiQ9CWR2.
KOiK11426.
OMAiVNTFTIC.
OrthoDBiEOG74XS68.
PhylomeDBiQ9CWR2.
TreeFamiTF106487.

Family and domain databases

InterProiIPR025805. Hist-Lys_N-MeTrfase_Smyd3.
IPR001214. SET_dom.
IPR002893. Znf_MYND.
[Graphical view]
PfamiPF00856. SET. 1 hit.
PF01753. zf-MYND. 1 hit.
[Graphical view]
SMARTiSM00317. SET. 1 hit.
[Graphical view]
PROSITEiPS51574. SAM_MT43_2. 1 hit.
PS50280. SET. 1 hit.
PS01360. ZF_MYND_1. 1 hit.
PS50865. ZF_MYND_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9CWR2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEALKVEKFT TANRGNGLRA VAPLRPGELL FRSDPLAYTV CKGSRGVVCD
60 70 80 90 100
RCLLGKEKLM RCSQCRIAKY CSAKCQKKAW PDHRRECSCL KSCKPRYPPD
110 120 130 140 150
SVRLLGRVIV KLMDEKPSES EKLYSFYDLE SNISKLTEDK KEGLRQLAMT
160 170 180 190 200
FQHFMREEIQ DASQLPPSFD LFEAFAKVIC NSFTICNAEM QEVGVGLYPS
210 220 230 240 250
MSLLNHSCDP NCSIVFNGPH LLLRAVREIE AGEELTICYL DMLMTSEERR
260 270 280 290 300
KQLRDQYCFE CDCIRCQTQD KDADMLTGDE QIWKEVQESL KKIEELKAHW
310 320 330 340 350
KWEQVLALCQ AIINSNSNRL PDINIYQLKV LDCAMDACIN LGMLEEALFY
360 370 380 390 400
AMRTMEPYRI FFPGSHPVRG VQVMKVGKLQ LHQGMFPQAM KNLRLAFDIM
410 420
KVTHGREHSL IEDLILLLEE CDANIRAS
Length:428
Mass (Da):49,126
Last modified:June 1, 2001 - v1
Checksum:i1EC765044E1FB0DA
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti318 – 3181N → D in AAH61485 (PubMed:15489334).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK010447 mRNA. Translation: BAB26947.1.
AK044168 mRNA. Translation: BAC31804.1.
AK046829 mRNA. Translation: BAC32887.1.
BC052431 mRNA. Translation: AAH52431.1.
BC061485 mRNA. Translation: AAH61485.1.
CCDSiCCDS15560.1.
RefSeqiNP_081464.1. NM_027188.3.
XP_006497044.1. XM_006496981.2.
XP_006497045.1. XM_006496982.2.
UniGeneiMm.222338.

Genome annotation databases

EnsembliENSMUST00000128302; ENSMUSP00000117410; ENSMUSG00000055067.
GeneIDi69726.
KEGGimmu:69726.
UCSCiuc007dvj.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK010447 mRNA. Translation: BAB26947.1.
AK044168 mRNA. Translation: BAC31804.1.
AK046829 mRNA. Translation: BAC32887.1.
BC052431 mRNA. Translation: AAH52431.1.
BC061485 mRNA. Translation: AAH61485.1.
CCDSiCCDS15560.1.
RefSeqiNP_081464.1. NM_027188.3.
XP_006497044.1. XM_006496981.2.
XP_006497045.1. XM_006496982.2.
UniGeneiMm.222338.

3D structure databases

ProteinModelPortaliQ9CWR2.
SMRiQ9CWR2. Positions 4-428.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi213640. 1 interaction.
STRINGi10090.ENSMUSP00000117410.

PTM databases

PhosphoSiteiQ9CWR2.

Proteomic databases

MaxQBiQ9CWR2.
PaxDbiQ9CWR2.
PRIDEiQ9CWR2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000128302; ENSMUSP00000117410; ENSMUSG00000055067.
GeneIDi69726.
KEGGimmu:69726.
UCSCiuc007dvj.1. mouse.

Organism-specific databases

CTDi64754.
MGIiMGI:1916976. Smyd3.

Phylogenomic databases

eggNOGiCOG2940.
GeneTreeiENSGT00530000063077.
HOGENOMiHOG000007850.
HOVERGENiHBG105004.
InParanoidiQ9CWR2.
KOiK11426.
OMAiVNTFTIC.
OrthoDBiEOG74XS68.
PhylomeDBiQ9CWR2.
TreeFamiTF106487.

Enzyme and pathway databases

BRENDAi2.1.1.43. 3474.
ReactomeiREACT_278269. PKMTs methylate histone lysines.

Miscellaneous databases

ChiTaRSiSmyd3. mouse.
NextBioi330194.
PROiQ9CWR2.
SOURCEiSearch...

Gene expression databases

BgeeiQ9CWR2.
CleanExiMM_SMYD3.
ExpressionAtlasiQ9CWR2. baseline and differential.
GenevisibleiQ9CWR2. MM.

Family and domain databases

InterProiIPR025805. Hist-Lys_N-MeTrfase_Smyd3.
IPR001214. SET_dom.
IPR002893. Znf_MYND.
[Graphical view]
PfamiPF00856. SET. 1 hit.
PF01753. zf-MYND. 1 hit.
[Graphical view]
SMARTiSM00317. SET. 1 hit.
[Graphical view]
PROSITEiPS51574. SAM_MT43_2. 1 hit.
PS50280. SET. 1 hit.
PS01360. ZF_MYND_1. 1 hit.
PS50865. ZF_MYND_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Brain cortex, Embryonic stem cell and Medulla oblongata.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6 and FVB/N-3.
    Tissue: Brain and Mammary tumor.

Entry informationi

Entry nameiSMYD3_MOUSE
AccessioniPrimary (citable) accession number: Q9CWR2
Secondary accession number(s): Q6P7V6, Q8BG90
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 16, 2003
Last sequence update: June 1, 2001
Last modified: June 24, 2015
This is version 101 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.