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Protein

N-lysine methyltransferase SMYD2

Gene

Smyd2

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

Functioni

Protein-lysine N-methyltransferase that methylates both histones and non-histone proteins, including p53/TP53 and RB1. Specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). Shows even higher methyltransferase activity on p53/TP53. Monomethylates 'Lys-370' of p53/TP53, leading to decreased DNA-binding activity and subsequent transcriptional regulation activity of p53/TP53. Monomethylates RB1 at 'Lys-860'.1 Publication

Catalytic activityi

S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei137 – 1371S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei240 – 2401Peptide substrate; via carbonyl oxygenBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri52 – 9039MYND-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Methyltransferase, Transferase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

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

Enzyme and pathway databases

BRENDAi2.1.1.43. 3474.
ReactomeiR-MMU-3214841. PKMTs methylate histone lysines.
R-MMU-6804760. Regulation of TP53 Activity through Methylation.

Names & Taxonomyi

Protein namesi
Recommended name:
N-lysine methyltransferase SMYD2 (EC:2.1.1.-)
Alternative name(s):
Histone methyltransferase SMYD2 (EC:2.1.1.43)
SET and MYND domain-containing protein 2
Gene namesi
Name:Smyd2
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 1

Organism-specific databases

MGIiMGI:1915889. Smyd2.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • cytosol Source: UniProtKB
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi240 – 2401Y → F: Abolishes methyltransferase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 433433N-lysine methyltransferase SMYD2PRO_0000218310Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei283 – 2831PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ8R5A0.
MaxQBiQ8R5A0.
PaxDbiQ8R5A0.
PeptideAtlasiQ8R5A0.
PRIDEiQ8R5A0.

PTM databases

iPTMnetiQ8R5A0.
PhosphoSiteiQ8R5A0.

Expressioni

Tissue specificityi

Highly expressed in heart, skeletal muscle and brain tissue. During cardiac development, it is differentially expressed with highest expression in the neonatal heart while very low expression is detected at E12.5 and adult. Specifically expressed in cardiomyocytes (at protein level).1 Publication

Gene expression databases

BgeeiQ8R5A0.
CleanExiMM_SMYD2.
GenevisibleiQ8R5A0. MM.

Interactioni

Subunit structurei

Interacts (via MYND-type zinc finger) with EPB41L3. Interacts (via SET domain) with p53/TP53. Interacts with RB1 and HSP90AA1 (By similarity). Interacts with RNA polymerase II and HELZ. Interacts with SIN3A and HDAC1.By similarity2 Publications

GO - Molecular functioni

  • p53 binding Source: MGI
  • RNA polymerase II core binding Source: UniProtKB

Protein-protein interaction databases

BioGridi230559. 2 interactions.
DIPiDIP-60503N.
STRINGi10090.ENSMUSP00000027897.

Structurei

Secondary structure

1
433
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi9 – 135Combined sources
Beta strandi19 – 257Combined sources
Beta strandi32 – 376Combined sources
Beta strandi39 – 435Combined sources
Helixi45 – 473Combined sources
Turni48 – 503Combined sources
Turni53 – 553Combined sources
Turni66 – 683Combined sources
Beta strandi72 – 754Combined sources
Helixi76 – 8611Combined sources
Turni87 – 893Combined sources
Helixi90 – 956Combined sources
Helixi104 – 11815Combined sources
Helixi124 – 1263Combined sources
Helixi131 – 1333Combined sources
Helixi138 – 1403Combined sources
Helixi143 – 16018Combined sources
Turni161 – 1633Combined sources
Helixi169 – 18214Combined sources
Beta strandi184 – 1874Combined sources
Beta strandi193 – 1986Combined sources
Helixi202 – 2043Combined sources
Beta strandi205 – 2073Combined sources
Beta strandi212 – 2187Combined sources
Beta strandi221 – 2288Combined sources
Beta strandi235 – 2384Combined sources
Helixi247 – 25812Combined sources
Helixi265 – 2695Combined sources
Helixi273 – 2764Combined sources
Helixi288 – 30821Combined sources
Turni309 – 3113Combined sources
Helixi314 – 32815Combined sources
Turni329 – 3313Combined sources
Helixi337 – 35216Combined sources
Helixi356 – 37318Combined sources
Helixi379 – 39416Combined sources
Helixi398 – 41518Combined sources
Helixi421 – 43111Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3QWVX-ray2.03A1-433[»]
3QWWX-ray1.80A1-433[»]
ProteinModelPortaliQ8R5A0.
SMRiQ8R5A0. Positions 3-432.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8R5A0.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini7 – 241235SETPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni17 – 193S-adenosyl-L-methionine bindingBy similarity
Regioni183 – 1853Peptide substrate bindingBy similarity
Regioni206 – 2072S-adenosyl-L-methionine bindingBy similarity
Regioni258 – 2603S-adenosyl-L-methionine bindingBy similarity

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily.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 fingeri52 – 9039MYND-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG2084. Eukaryota.
COG2940. LUCA.
GeneTreeiENSGT00530000063077.
HOGENOMiHOG000007850.
HOVERGENiHBG098536.
InParanoidiQ8R5A0.
KOiK11426.
OMAiHPERTQS.
OrthoDBiEOG74XS68.
PhylomeDBiQ8R5A0.
TreeFamiTF106487.

Family and domain databases

Gene3Di1.25.40.10. 1 hit.
InterProiIPR001214. SET_dom.
IPR011990. TPR-like_helical_dom.
IPR002893. Znf_MYND.
[Graphical view]
PfamiPF00856. SET. 1 hit.
PF01753. zf-MYND. 1 hit.
[Graphical view]
SUPFAMiSSF48452. SSF48452. 1 hit.
PROSITEiPS50280. SET. 1 hit.
PS01360. ZF_MYND_1. 1 hit.
PS50865. ZF_MYND_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8R5A0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRAEARGGLE RFCSAGKGRG LRALRPFHVG DLLFSCPAYA CVLTVGERGH
60 70 80 90 100
HCECCFARKE GLSKCGRCKQ AFYCDVECQK EDWPLHKLEC SSMVVLGENW
110 120 130 140 150
NPSETVRLTA RILAKQKIHP ERTPSEKLLA VREFESHLDK LDNEKKDLIQ
160 170 180 190 200
SDIAALHQFY SKYLEFPDHS SLVVLFAQVN CNGFTIEDEE LSHLGSAIFP
210 220 230 240 250
DVALMNHSCC PNVIVTYKGT LAEVRAVQEI HPGDEVFTSY IDLLYPTEDR
260 270 280 290 300
NDRLRDSYFF TCECRECTTK DKDKAKVEVR KLSSPPQAEA IRDMVRYARN
310 320 330 340 350
VIEEFRRAKH YKSPSELLEI CELSQEKMSS VFEDSNVYML HMMYQAMGVC
360 370 380 390 400
LYMQDWEGAL KYGQKIIKPY SKHYPVYSLN VASMWLKLGR LYMGLENKAA
410 420 430
GEKALKKAIA IMEVAHGKDH PYISEIKQEI ESH
Length:433
Mass (Da):49,567
Last modified:June 1, 2002 - v1
Checksum:i5978E9A3FC2CDCE4
GO

Sequence cautioni

The sequence BAE29912.1 differs from that shown.Deletion within an exon that does not correspond to an intron.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK150857 mRNA. Translation: BAE29912.1. Sequence problems.
BC023119 mRNA. Translation: AAH23119.1.
CCDSiCCDS35821.1.
RefSeqiNP_081072.1. NM_026796.1.
UniGeneiMm.156895.

Genome annotation databases

EnsembliENSMUST00000027897; ENSMUSP00000027897; ENSMUSG00000026603.
GeneIDi226830.
KEGGimmu:226830.
UCSCiuc007eax.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK150857 mRNA. Translation: BAE29912.1. Sequence problems.
BC023119 mRNA. Translation: AAH23119.1.
CCDSiCCDS35821.1.
RefSeqiNP_081072.1. NM_026796.1.
UniGeneiMm.156895.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3QWVX-ray2.03A1-433[»]
3QWWX-ray1.80A1-433[»]
ProteinModelPortaliQ8R5A0.
SMRiQ8R5A0. Positions 3-432.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi230559. 2 interactions.
DIPiDIP-60503N.
STRINGi10090.ENSMUSP00000027897.

PTM databases

iPTMnetiQ8R5A0.
PhosphoSiteiQ8R5A0.

Proteomic databases

EPDiQ8R5A0.
MaxQBiQ8R5A0.
PaxDbiQ8R5A0.
PeptideAtlasiQ8R5A0.
PRIDEiQ8R5A0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000027897; ENSMUSP00000027897; ENSMUSG00000026603.
GeneIDi226830.
KEGGimmu:226830.
UCSCiuc007eax.1. mouse.

Organism-specific databases

CTDi56950.
MGIiMGI:1915889. Smyd2.

Phylogenomic databases

eggNOGiKOG2084. Eukaryota.
COG2940. LUCA.
GeneTreeiENSGT00530000063077.
HOGENOMiHOG000007850.
HOVERGENiHBG098536.
InParanoidiQ8R5A0.
KOiK11426.
OMAiHPERTQS.
OrthoDBiEOG74XS68.
PhylomeDBiQ8R5A0.
TreeFamiTF106487.

Enzyme and pathway databases

BRENDAi2.1.1.43. 3474.
ReactomeiR-MMU-3214841. PKMTs methylate histone lysines.
R-MMU-6804760. Regulation of TP53 Activity through Methylation.

Miscellaneous databases

ChiTaRSiSmyd2. mouse.
EvolutionaryTraceiQ8R5A0.
PROiQ8R5A0.
SOURCEiSearch...

Gene expression databases

BgeeiQ8R5A0.
CleanExiMM_SMYD2.
GenevisibleiQ8R5A0. MM.

Family and domain databases

Gene3Di1.25.40.10. 1 hit.
InterProiIPR001214. SET_dom.
IPR011990. TPR-like_helical_dom.
IPR002893. Znf_MYND.
[Graphical view]
PfamiPF00856. SET. 1 hit.
PF01753. zf-MYND. 1 hit.
[Graphical view]
SUPFAMiSSF48452. SSF48452. 1 hit.
PROSITEiPS50280. SET. 1 hit.
PS01360. ZF_MYND_1. 1 hit.
PS50865. ZF_MYND_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: Bone marrow.
  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].
  3. "Identification and characterization of Smyd2: a split SET/MYND domain-containing histone H3 lysine 36-specific methyltransferase that interacts with the Sin3 histone deacetylase complex."
    Brown M.A., Sims R.J. III, Gottlieb P.D., Tucker P.W.
    Mol. Cancer 5:26-26(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, MUTAGENESIS OF TYR-240, INTERACTION WITH SIN3A AND HDAC1.
  4. Cited for: TISSUE SPECIFICITY, INTERACTION WITH RNA POLYMERASE II AND HELZ, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiSMYD2_MOUSE
AccessioniPrimary (citable) accession number: Q8R5A0
Secondary accession number(s): Q3UBQ2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 10, 2004
Last sequence update: June 1, 2002
Last modified: July 6, 2016
This is version 99 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

Although specifically expressed in cardiomyocytes, a conditional deletion in heart does not lead to any visible phenotype.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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

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 one 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.