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Protein

Histone-lysine N-methyltransferase Smyd1

Gene

Smyd1

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

Functioni

Methylates histone H3 at 'Lys-4' (H3K4me). Acts as a transcriptional repressor. Essential for cardiomyocyte differentiation and cardiac morphogenesis.2 Publications

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)DescriptionActionsGraphical viewLength
Binding sitei135S-adenosyl-L-methionine1
Metal bindingi208Zinc1
Metal bindingi274Zinc1
Metal bindingi276Zinc1
Metal bindingi279Zinc1

Regions

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

GO - Molecular functioni

GO - Biological processi

  • chromatin remodeling Source: MGI
  • heart development Source: MGI
  • negative regulation of transcription, DNA-templated Source: MGI
  • positive regulation of myoblast differentiation Source: MGI
  • positive regulation of myotube differentiation Source: MGI
  • skeletal muscle cell differentiation Source: MGI
  • transcription, DNA-templated Source: UniProtKB-KW
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):
CD8b-opposite
SET and MYND domain-containing protein 1
Zinc finger protein BOP
Short name:
m-BOP
Gene namesi
Name:Smyd1
Synonyms:Bop
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 6

Organism-specific databases

MGIiMGI:104790. Smyd1.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: MGI
  • nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002183081 – 490Histone-lysine N-methyltransferase Smyd1Add BLAST490

Proteomic databases

MaxQBiP97443.
PaxDbiP97443.
PRIDEiP97443.

PTM databases

iPTMnetiP97443.
PhosphoSitePlusiP97443.

Expressioni

Tissue specificityi

Expressed in cardiac and skeletal muscle, lymphocytes and thymus.2 Publications

Gene expression databases

BgeeiENSMUSG00000055027.
CleanExiMM_SMYD1.
ExpressionAtlasiP97443. baseline and differential.
GenevisibleiP97443. MM.

Interactioni

Subunit structurei

Interacts with HDAC1, HDAC2 and HDAC3. Interacts (via MYND-type zinc finger) with NACA isoform skNAC.2 Publications

Protein-protein interaction databases

BioGridi198379. 5 interactors.
IntActiP97443. 1 interactor.
MINTiMINT-4134971.
STRINGi10090.ENSMUSP00000073911.

Structurei

Secondary structure

1490
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi9 – 13Combined sources5
Beta strandi15 – 17Combined sources3
Beta strandi19 – 25Combined sources7
Beta strandi32 – 36Combined sources5
Beta strandi39 – 43Combined sources5
Helixi45 – 47Combined sources3
Turni48 – 50Combined sources3
Turni53 – 55Combined sources3
Turni66 – 68Combined sources3
Beta strandi72 – 75Combined sources4
Helixi76 – 96Combined sources21
Helixi102 – 116Combined sources15
Beta strandi119 – 121Combined sources3
Beta strandi126 – 128Combined sources3
Helixi129 – 131Combined sources3
Helixi136 – 138Combined sources3
Helixi141 – 157Combined sources17
Helixi167 – 178Combined sources12
Beta strandi181 – 185Combined sources5
Beta strandi191 – 197Combined sources7
Helixi201 – 203Combined sources3
Beta strandi211 – 217Combined sources7
Beta strandi222 – 224Combined sources3
Helixi228 – 230Combined sources3
Beta strandi233 – 240Combined sources8
Helixi259 – 270Combined sources12
Helixi277 – 281Combined sources5
Turni282 – 284Combined sources3
Helixi285 – 288Combined sources4
Beta strandi293 – 295Combined sources3
Helixi299 – 320Combined sources22
Turni321 – 323Combined sources3
Helixi325 – 339Combined sources15
Turni340 – 342Combined sources3
Helixi348 – 363Combined sources16
Helixi367 – 384Combined sources18
Helixi390 – 405Combined sources16
Helixi409 – 426Combined sources18
Helixi432 – 465Combined sources34

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3N71X-ray2.30A1-490[»]
ProteinModelPortaliP97443.
SMRiP97443.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP97443.

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 binding3
Regioni205 – 206S-adenosyl-L-methionine binding2
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.

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 annotationCurated

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.
InParanoidiP97443.
KOiK11426.
OMAiVTHGPTH.
OrthoDBiEOG091G066T.
PhylomeDBiP97443.
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]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P97443-1) [UniParc]FASTAAdd to basket
Also known as: ISKM-BOP11 Publication

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MTIGSMENVE VFTSEGKGRG LKATKEFWAA DVIFAERAYS AVVFDSLINF
60 70 80 90 100
VCHTCFKRQE KLHRCGQCKF AHYCDRTCQK DAWLNHKNEC AAIKKYGKVP
110 120 130 140 150
NENIRLAARI MWRVEREGTG LTEGCLVSVD DLQNHVEHFG EEEQKELRVD
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
SYIDFLHLSE ERRRQLKKQY YFDCSCEHCQ KGLKDDLFLA AKEDPKPSQE
310 320 330 340 350
VVKEMIQFSK DTLEKIDKAR SEGLYHEVVK LCRECLEKQE PVFADTNLYV
360 370 380 390 400
LRLLSIASEV LSYLQAYEEA SHYARRMVDG YMKLYHHNNA QLGMAVMRAG
410 420 430 440 450
LTNWHAGHIE VGHGMICKAY AILLVTHGPS HPITKDLEAM RMQTEMELRM
460 470 480 490
FRQNEFMYHK MREAALNNQP MQVMAEPSNE PAPALFHKKQ
Length:490
Mass (Da):56,496
Last modified:May 3, 2011 - v3
Checksum:i5D18208678771CBE
GO
Isoform 2 (identifier: P97443-2) [UniParc]FASTAAdd to basket
Also known as: SKM-BOP21 Publication

The sequence of this isoform differs from the canonical sequence as follows:
     220-220: N → K
     221-233: Missing.

Show »
Length:477
Mass (Da):54,926
Checksum:iA927C87FA4B6CAC7
GO
Isoform 3 (identifier: P97443-3) [UniParc]FASTAAdd to basket
Also known as: T-BOP1 Publication

The sequence of this isoform differs from the canonical sequence as follows:
     6-45: MENVEVFTSEGKGRGLKATKEFWAADVIFAERAYSAVVFD → MKNGEACGGWQ

Show »
Length:461
Mass (Da):53,206
Checksum:i782D59F2992BBA22
GO

Sequence cautioni

The sequence AAC53021 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAC53022 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti95K → R in strain: C57BL/6. 1 Publication1
Natural varianti160P → L in strain: C57BL/6. 1 Publication1
Natural varianti344A → T in strain: C57BL/6. 1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0504026 – 45MENVE…AVVFD → MKNGEACGGWQ in isoform 3. 1 PublicationAdd BLAST40
Alternative sequenceiVSP_050403220N → K in isoform 2. 1 Publication1
Alternative sequenceiVSP_050404221 – 233Missing in isoform 2. 1 PublicationAdd BLAST13

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U76371 mRNA. Translation: AAC53020.1.
U76373 mRNA. Translation: AAC53021.2. Different initiation.
U76374 mRNA. Translation: AAC53022.2. Different initiation.
AK142252 mRNA. Translation: BAE24995.1.
CH466523 Genomic DNA. Translation: EDK98934.1.
BC076601 mRNA. Translation: AAH76601.1.
CCDSiCCDS20227.2. [P97443-2]
CCDS51805.1. [P97443-1]
RefSeqiNP_001153599.1. NM_001160127.1. [P97443-1]
NP_033892.2. NM_009762.2. [P97443-2]
UniGeneiMm.234274.
Mm.440892.

Genome annotation databases

EnsembliENSMUST00000074301; ENSMUSP00000073911; ENSMUSG00000055027. [P97443-1]
ENSMUST00000114186; ENSMUSP00000109824; ENSMUSG00000055027. [P97443-2]
GeneIDi12180.
KEGGimmu:12180.
UCSCiuc009cgj.2. mouse. [P97443-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U76371 mRNA. Translation: AAC53020.1.
U76373 mRNA. Translation: AAC53021.2. Different initiation.
U76374 mRNA. Translation: AAC53022.2. Different initiation.
AK142252 mRNA. Translation: BAE24995.1.
CH466523 Genomic DNA. Translation: EDK98934.1.
BC076601 mRNA. Translation: AAH76601.1.
CCDSiCCDS20227.2. [P97443-2]
CCDS51805.1. [P97443-1]
RefSeqiNP_001153599.1. NM_001160127.1. [P97443-1]
NP_033892.2. NM_009762.2. [P97443-2]
UniGeneiMm.234274.
Mm.440892.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3N71X-ray2.30A1-490[»]
ProteinModelPortaliP97443.
SMRiP97443.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi198379. 5 interactors.
IntActiP97443. 1 interactor.
MINTiMINT-4134971.
STRINGi10090.ENSMUSP00000073911.

PTM databases

iPTMnetiP97443.
PhosphoSitePlusiP97443.

Proteomic databases

MaxQBiP97443.
PaxDbiP97443.
PRIDEiP97443.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000074301; ENSMUSP00000073911; ENSMUSG00000055027. [P97443-1]
ENSMUST00000114186; ENSMUSP00000109824; ENSMUSG00000055027. [P97443-2]
GeneIDi12180.
KEGGimmu:12180.
UCSCiuc009cgj.2. mouse. [P97443-1]

Organism-specific databases

CTDi150572.
MGIiMGI:104790. Smyd1.

Phylogenomic databases

eggNOGiKOG2084. Eukaryota.
COG2940. LUCA.
GeneTreeiENSGT00530000063077.
HOGENOMiHOG000050244.
HOVERGENiHBG054953.
InParanoidiP97443.
KOiK11426.
OMAiVTHGPTH.
OrthoDBiEOG091G066T.
PhylomeDBiP97443.
TreeFamiTF106487.

Miscellaneous databases

ChiTaRSiSmyd1. mouse.
EvolutionaryTraceiP97443.
PROiP97443.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000055027.
CleanExiMM_SMYD1.
ExpressionAtlasiP97443. baseline and differential.
GenevisibleiP97443. MM.

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...

Entry informationi

Entry nameiSMYD1_MOUSE
AccessioniPrimary (citable) accession number: P97443
Secondary accession number(s): P97442, P97444, Q6DFW7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 19, 2003
Last sequence update: May 3, 2011
Last modified: November 2, 2016
This is version 124 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

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.