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Protein

Histone-lysine N-methyltransferase SMYD1

Gene

SMYD1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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 + N6-methyl-L-lysine-[histone].

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei135S-adenosyl-L-methioninePROSITE-ProRule annotation1
Metal bindingi208ZincPROSITE-ProRule annotation1
Metal bindingi274ZincPROSITE-ProRule annotation1
Metal bindingi276ZincPROSITE-ProRule annotation1
Metal bindingi279ZincPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri52 – 90MYND-typePROSITE-ProRule annotationAdd BLAST39

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Methyltransferase, Repressor, Transferase
Biological processTranscription, Transcription regulation
LigandMetal-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

EuPathDBiHostDB:ENSG00000115593.14
HGNCiHGNC:20986 SMYD1
MIMi606846 gene
neXtProtiNX_Q8NB12

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi150572
OpenTargetsiENSG00000115593
PharmGKBiPA134862943

Polymorphism and mutation databases

BioMutaiSMYD1
DMDMi34925329

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002183071 – 490Histone-lysine N-methyltransferase SMYD1Add BLAST490

Proteomic databases

PaxDbiQ8NB12
PeptideAtlasiQ8NB12
PRIDEiQ8NB12
ProteomicsDBi72714

PTM databases

iPTMnetiQ8NB12
PhosphoSitePlusiQ8NB12

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

BgeeiENSG00000115593 Expressed in 110 organ(s), highest expression level in quadriceps femoris
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

Protein-protein interaction databases

BioGridi127308, 18 interactors
IntActiQ8NB12, 42 interactors
MINTiQ8NB12
STRINGi9606.ENSP00000393453

Structurei

3D structure databases

ProteinModelPortaliQ8NB12
SMRiQ8NB12
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini7 – 253SETPROSITE-ProRule annotationAdd BLAST247

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni17 – 19S-adenosyl-L-methionine bindingBy similarity3
Regioni205 – 206S-adenosyl-L-methionine bindingBy similarity2
Regioni270 – 272S-adenosyl-L-methionine bindingBy similarity3

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

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri52 – 90MYND-typePROSITE-ProRule annotationAdd BLAST39

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG2084 Eukaryota
COG2940 LUCA
GeneTreeiENSGT00530000063077
HOGENOMiHOG000050244
HOVERGENiHBG054953
InParanoidiQ8NB12
KOiK11426
OMAiGIFPNLC
OrthoDBiEOG091G066T
PhylomeDBiQ8NB12
TreeFamiTF106487

Family and domain databases

Gene3Di1.25.40.10, 1 hit
InterProiView protein in InterPro
IPR001214 SET_dom
IPR011990 TPR-like_helical_dom_sf
IPR002893 Znf_MYND
PfamiView protein in Pfam
PF00856 SET, 1 hit
PF01753 zf-MYND, 1 hit
SMARTiView protein in SMART
SM00317 SET, 1 hit
PROSITEiView protein in PROSITE
PS50280 SET, 1 hit
PS01360 ZF_MYND_1, 1 hit
PS50865 ZF_MYND_2, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 2 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
C9JUP3C9JUP3_HUMAN
Histone-lysine N-methyltransferase ...
SMYD1
103Annotation score:
E9PHG3E9PHG3_HUMAN
Histone-lysine N-methyltransferase ...
SMYD1
477Annotation score:

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_052990164Q → P. Corresponds to variant dbSNP:rs1542087Ensembl.1

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

Similar proteinsi

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
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi127308, 18 interactors
IntActiQ8NB12, 42 interactors
MINTiQ8NB12
STRINGi9606.ENSP00000393453

PTM databases

iPTMnetiQ8NB12
PhosphoSitePlusiQ8NB12

Polymorphism and mutation databases

BioMutaiSMYD1
DMDMi34925329

Proteomic databases

PaxDbiQ8NB12
PeptideAtlasiQ8NB12
PRIDEiQ8NB12
ProteomicsDBi72714

Protocols and materials databases

DNASUi150572
Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi150572
DisGeNETi150572
EuPathDBiHostDB:ENSG00000115593.14
GeneCardsiSMYD1
HGNCiHGNC:20986 SMYD1
HPAiHPA062282
MIMi606846 gene
neXtProtiNX_Q8NB12
OpenTargetsiENSG00000115593
PharmGKBiPA134862943
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2084 Eukaryota
COG2940 LUCA
GeneTreeiENSGT00530000063077
HOGENOMiHOG000050244
HOVERGENiHBG054953
InParanoidiQ8NB12
KOiK11426
OMAiGIFPNLC
OrthoDBiEOG091G066T
PhylomeDBiQ8NB12
TreeFamiTF106487

Miscellaneous databases

GenomeRNAii150572
PROiPR:Q8NB12
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000115593 Expressed in 110 organ(s), highest expression level in quadriceps femoris
CleanExiHS_SMYD1
ExpressionAtlasiQ8NB12 baseline and differential
GenevisibleiQ8NB12 HS

Family and domain databases

Gene3Di1.25.40.10, 1 hit
InterProiView protein in InterPro
IPR001214 SET_dom
IPR011990 TPR-like_helical_dom_sf
IPR002893 Znf_MYND
PfamiView protein in Pfam
PF00856 SET, 1 hit
PF01753 zf-MYND, 1 hit
SMARTiView protein in SMART
SM00317 SET, 1 hit
PROSITEiView protein in PROSITE
PS50280 SET, 1 hit
PS01360 ZF_MYND_1, 1 hit
PS50865 ZF_MYND_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiSMYD1_HUMAN
AccessioniPrimary (citable) accession number: Q8NB12
Secondary accession number(s): A0AV30, A6NE13
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 19, 2003
Last sequence update: October 1, 2002
Last modified: November 7, 2018
This is version 128 of the entry and version 1 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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