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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei135 – 1351S-adenosyl-L-methionine
Metal bindingi208 – 2081Zinc
Metal bindingi274 – 2741Zinc
Metal bindingi276 – 2761Zinc
Metal bindingi279 – 2791Zinc

Regions

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

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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 490490Histone-lysine N-methyltransferase Smyd1PRO_0000218308Add
BLAST

Proteomic databases

MaxQBiP97443.
PaxDbiP97443.
PRIDEiP97443.

PTM databases

iPTMnetiP97443.
PhosphoSiteiP97443.

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 interactions.
IntActiP97443. 1 interaction.
MINTiMINT-4134971.
STRINGi10090.ENSMUSP00000073911.

Structurei

Secondary structure

1
490
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi9 – 135Combined sources
Beta strandi15 – 173Combined sources
Beta strandi19 – 257Combined sources
Beta strandi32 – 365Combined sources
Beta strandi39 – 435Combined sources
Helixi45 – 473Combined sources
Turni48 – 503Combined sources
Turni53 – 553Combined sources
Turni66 – 683Combined sources
Beta strandi72 – 754Combined sources
Helixi76 – 9621Combined sources
Helixi102 – 11615Combined sources
Beta strandi119 – 1213Combined sources
Beta strandi126 – 1283Combined sources
Helixi129 – 1313Combined sources
Helixi136 – 1383Combined sources
Helixi141 – 15717Combined sources
Helixi167 – 17812Combined sources
Beta strandi181 – 1855Combined sources
Beta strandi191 – 1977Combined sources
Helixi201 – 2033Combined sources
Beta strandi211 – 2177Combined sources
Beta strandi222 – 2243Combined sources
Helixi228 – 2303Combined sources
Beta strandi233 – 2408Combined sources
Helixi259 – 27012Combined sources
Helixi277 – 2815Combined sources
Turni282 – 2843Combined sources
Helixi285 – 2884Combined sources
Beta strandi293 – 2953Combined sources
Helixi299 – 32022Combined sources
Turni321 – 3233Combined sources
Helixi325 – 33915Combined sources
Turni340 – 3423Combined sources
Helixi348 – 36316Combined sources
Helixi367 – 38418Combined sources
Helixi390 – 40516Combined sources
Helixi409 – 42618Combined sources
Helixi432 – 46534Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3N71X-ray2.30A1-490[»]
ProteinModelPortaliP97443.
SMRiP97443. Positions 1-468.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP97443.

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 binding
Regioni205 – 2062S-adenosyl-L-methionine binding
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.

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)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri52 – 9039MYND-typePROSITE-ProRule annotationAdd
BLAST

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)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti95 – 951K → R in strain: C57BL/6. 1 Publication
Natural varianti160 – 1601P → L in strain: C57BL/6. 1 Publication
Natural varianti344 – 3441A → T in strain: C57BL/6. 1 Publication

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei6 – 4540MENVE…AVVFD → MKNGEACGGWQ in isoform 3. 1 PublicationVSP_050402Add
BLAST
Alternative sequencei220 – 2201N → K in isoform 2. 1 PublicationVSP_050403
Alternative sequencei221 – 23313Missing in isoform 2. 1 PublicationVSP_050404Add
BLAST

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
EntryMethodResolution (Å)ChainPositionsPDBsum
3N71X-ray2.30A1-490[»]
ProteinModelPortaliP97443.
SMRiP97443. Positions 1-468.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi198379. 5 interactions.
IntActiP97443. 1 interaction.
MINTiMINT-4134971.
STRINGi10090.ENSMUSP00000073911.

PTM databases

iPTMnetiP97443.
PhosphoSiteiP97443.

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: September 7, 2016
This is version 122 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.