Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Histone-lysine N-methyltransferase SMYD1

Gene

SMYD1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Methylates histone H3 at 'Lys-4' (H3K4me), seems able to perform both mono-, di-, and trimethylation. Acts as a transcriptional repressor. Essential for cardiomyocyte differentiation and cardiac morphogenesis.

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei135 – 1351S-adenosyl-L-methioninePROSITE-ProRule annotation
Metal bindingi208 – 2081ZincPROSITE-ProRule annotation
Metal bindingi274 – 2741ZincPROSITE-ProRule annotation
Metal bindingi276 – 2761ZincPROSITE-ProRule annotation
Metal bindingi279 – 2791ZincPROSITE-ProRule annotation

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

Methyltransferase, Repressor, Transferase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

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

Names & Taxonomyi

Protein namesi
Recommended name:
Histone-lysine N-methyltransferase SMYD1 (EC:2.1.1.43)
Alternative name(s):
SET and MYND domain-containing protein 1
Gene namesi
Name:SMYD1
OrganismiHomo sapiens (Human)Imported
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:20986. SMYD1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134862943.

Polymorphism and mutation databases

BioMutaiSMYD1.
DMDMi34925329.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 490490Histone-lysine N-methyltransferase SMYD1PRO_0000218307Add
BLAST

Proteomic databases

PaxDbiQ8NB12.
PRIDEiQ8NB12.

PTM databases

PhosphoSiteiQ8NB12.

Expressioni

Tissue specificityi

Expression seems mostly restricted to heart and skeletal muscle.1 Publication

Inductioni

By serum response factor SRF and myogenin. SRF binds to the CArG site and MYOG binds to the E-box element on SMYD1 promoter.1 Publication

Gene expression databases

BgeeiQ8NB12.
CleanExiHS_SMYD1.
ExpressionAtlasiQ8NB12. baseline and differential.
GenevisibleiQ8NB12. HS.

Organism-specific databases

HPAiHPA062282.

Interactioni

Subunit structurei

Interacts with HDAC1, HDAC2 and HDAC3. Interacts (via MYND-type zinc finger) with NACA isoform skNAC (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
ADSSP305202EBI-8463848,EBI-1042898
BHLHE40O145033EBI-8463848,EBI-711810
HOMEZQ8IX15-33EBI-8463848,EBI-10172004
MYH7BA7E2Y12EBI-8463848,EBI-2880253
RBM4BQ9BQ042EBI-8463848,EBI-715531
ZBTB44Q8NCP53EBI-8463848,EBI-5658292

Protein-protein interaction databases

BioGridi127308. 18 interactions.
IntActiQ8NB12. 16 interactions.
STRINGi9606.ENSP00000393453.

Structurei

3D structure databases

ProteinModelPortaliQ8NB12.
SMRiQ8NB12. Positions 1-468.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini7 – 253247SETPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni17 – 193S-adenosyl-L-methionine bindingBy similarity
Regioni205 – 2062S-adenosyl-L-methionine bindingBy similarity
Regioni270 – 2723S-adenosyl-L-methionine bindingBy similarity

Domaini

The SET domain is split between the S-sequence (residues 1-49) and the core SET domain (residues 181-258), however the two segments still come together to form a conserved SET domain fold.By similarity

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation
Contains 1 MYND-type zinc finger.PROSITE-ProRule annotationCurated
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.
HOGENOMiHOG000050244.
HOVERGENiHBG054953.
InParanoidiQ8NB12.
KOiK11426.
OMAiVTHGPTH.
PhylomeDBiQ8NB12.
TreeFamiTF106487.

Family and domain databases

InterProiIPR001214. SET_dom.
IPR002893. Znf_MYND.
[Graphical view]
PfamiPF00856. SET. 1 hit.
PF01753. zf-MYND. 1 hit.
[Graphical view]
SMARTiSM00317. SET. 1 hit.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
PS01360. ZF_MYND_1. 1 hit.
PS50865. ZF_MYND_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8NB12-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTIGRMENVE VFTAEGKGRG LKATKEFWAA DIIFAERAYS AVVFDSLVNF
60 70 80 90 100
VCHTCFKRQE KLHRCGQCKF AHYCDRTCQK DAWLNHKNEC SAIKRYGKVP
110 120 130 140 150
NENIRLAARI MWRVEREGTG LTEGCLVSVD DLQNHVEHFG EEEQKDLRVD
160 170 180 190 200
VDTFLQYWPP QSQQFSMQYI SHIFGVINCN GFTLSDQRGL QAVGVGIFPN
210 220 230 240 250
LGLVNHDCWP NCTVIFNNGN HEAVKSMFHT QMRIELRALG KISEGEELTV
260 270 280 290 300
SYIDFLNVSE ERKRQLKKQY YFDCTCEHCQ KKLKDDLFLG VKDNPKPSQE
310 320 330 340 350
VVKEMIQFSK DTLEKIDKAR SEGLYHEVVK LCRECLEKQE PVFADTNIYM
360 370 380 390 400
LRMLSIVSEV LSYLQAFEEA SFYARRMVDG YMKLYHPNNA QLGMAVMRAG
410 420 430 440 450
LTNWHAGNIE VGHGMICKAY AILLVTHGPS HPITKDLEAM RVQTEMELRM
460 470 480 490
FRQNEFMYYK MREAALNNQP MQVMAEPSNE PSPALFHKKQ
Length:490
Mass (Da):56,617
Last modified:October 1, 2002 - v1
Checksum:i1AE2FAE62D2B28C6
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti164 – 1641Q → P.
Corresponds to variant rs1542087 [ dbSNP | Ensembl ].
VAR_052990

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK091724 mRNA. Translation: BAC03732.1.
AL832035 mRNA. Translation: CAI46139.1.
AC092836 Genomic DNA. No translation available.
BC126191 mRNA. Translation: AAI26192.1.
CCDSiCCDS33240.1.
RefSeqiNP_938015.1. NM_198274.3.
UniGeneiHs.516176.

Genome annotation databases

EnsembliENST00000419482; ENSP00000393453; ENSG00000115593.
GeneIDi150572.
KEGGihsa:150572.
UCSCiuc002ssr.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK091724 mRNA. Translation: BAC03732.1.
AL832035 mRNA. Translation: CAI46139.1.
AC092836 Genomic DNA. No translation available.
BC126191 mRNA. Translation: AAI26192.1.
CCDSiCCDS33240.1.
RefSeqiNP_938015.1. NM_198274.3.
UniGeneiHs.516176.

3D structure databases

ProteinModelPortaliQ8NB12.
SMRiQ8NB12. Positions 1-468.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi127308. 18 interactions.
IntActiQ8NB12. 16 interactions.
STRINGi9606.ENSP00000393453.

PTM databases

PhosphoSiteiQ8NB12.

Polymorphism and mutation databases

BioMutaiSMYD1.
DMDMi34925329.

Proteomic databases

PaxDbiQ8NB12.
PRIDEiQ8NB12.

Protocols and materials databases

DNASUi150572.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000419482; ENSP00000393453; ENSG00000115593.
GeneIDi150572.
KEGGihsa:150572.
UCSCiuc002ssr.4. human.

Organism-specific databases

CTDi150572.
GeneCardsiSMYD1.
HGNCiHGNC:20986. SMYD1.
HPAiHPA062282.
MIMi606846. gene.
neXtProtiNX_Q8NB12.
PharmGKBiPA134862943.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2084. Eukaryota.
COG2940. LUCA.
GeneTreeiENSGT00530000063077.
HOGENOMiHOG000050244.
HOVERGENiHBG054953.
InParanoidiQ8NB12.
KOiK11426.
OMAiVTHGPTH.
PhylomeDBiQ8NB12.
TreeFamiTF106487.

Miscellaneous databases

GenomeRNAii150572.
NextBioi86471.
PROiQ8NB12.
SOURCEiSearch...

Gene expression databases

BgeeiQ8NB12.
CleanExiHS_SMYD1.
ExpressionAtlasiQ8NB12. baseline and differential.
GenevisibleiQ8NB12. HS.

Family and domain databases

InterProiIPR001214. SET_dom.
IPR002893. Znf_MYND.
[Graphical view]
PfamiPF00856. SET. 1 hit.
PF01753. zf-MYND. 1 hit.
[Graphical view]
SMARTiSM00317. SET. 1 hit.
[Graphical view]
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. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Heart.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Skeletal muscle.
  3. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
    , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "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].
  5. "SMYD1, the myogenic activator, is a direct target of serum response factor and myogenin."
    Li D., Niu Z., Yu W., Qian Y., Wang Q., Li Q., Yi Z., Luo J., Wu X., Wang Y., Schwartz R.J., Liu M.
    Nucleic Acids Res. 37:7059-7071(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, INDUCTION BY SRF.

Entry informationi

Entry nameiSMYD1_HUMAN
AccessioniPrimary (citable) accession number: Q8NB12
Secondary accession number(s): A0AV30, A6NE13
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 19, 2003
Last sequence update: October 1, 2002
Last modified: March 16, 2016
This is version 113 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. 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.