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Q9H7B4 (SMYD3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 118. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Histone-lysine N-methyltransferase SMYD3

EC=2.1.1.43
Alternative name(s):
SET and MYND domain-containing protein 3
Zinc finger MYND domain-containing protein 1
Gene names
Name:SMYD3
Synonyms:ZMYND1, ZNFN3A1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length428 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Histone methyltransferase. Specifically methylates 'Lys-4' and 'Lys-5' of histone H3, inducing di- and tri-methylation, but not monomethylation. Plays an important role in transcriptional activation as a member of an RNA polymerase complex. Binds DNA containing 5'-CCCTCC-3' or 5'-GAGGGG-3' sequences. Ref.1 Ref.8

Catalytic activity

S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone]. Ref.1 Ref.8

Enzyme regulation

Histone methyltransferase activity strongly stimulated by HSPCA.

Subunit structure

Interacts with HSPCA. Interacts with HELZ. Interacts with POLR2A; the interaction may be indirect and may be mediated by HELZ. Ref.1

Subcellular location

Cytoplasm. Nucleus. Note: Mainly cytoplasmic when cells are arrested at G0/G1. Accumulates in the nucleus at S phase and G2/M. Ref.1

Tissue specificity

Expressed in skeletal muscles and testis. Overexpressed in a majority of colorectal and hepatocellular carcinomas. Ref.1

Sequence similarities

Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family.

Contains 1 MYND-type zinc finger.

Contains 1 SET domain.

Sequence caution

The sequence CAI14744.1 differs from that shown. Reason: Erroneous initiation.

The sequence CAI16628.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
   Cellular componentCytoplasm
Nucleus
   Coding sequence diversityAlternative splicing
   DomainZinc-finger
   LigandMetal-binding
S-adenosyl-L-methionine
Zinc
   Molecular functionChromatin regulator
Methyltransferase
Transferase
   PTMAcetylation
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

nucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionhistone-lysine N-methyltransferase activity

Inferred from sequence or structural similarity. Source: UniProtKB

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9H7B4-1)

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.
Isoform 2 (identifier: Q9H7B4-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-170: Missing.
     171-176: LFEAFA → MEEEEE
Note: No experimental confirmation available.
Isoform 3 (identifier: Q9H7B4-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-59: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 428428Histone-lysine N-methyltransferase SMYD3
PRO_0000218312

Regions

Domain4 – 240237SET
Zinc finger49 – 8739MYND-type
Region14 – 163S-adenosyl-L-methionine binding
Region205 – 2062S-adenosyl-L-methionine binding

Sites

Binding site1241S-adenosyl-L-methionine
Binding site1321S-adenosyl-L-methionine
Binding site1811S-adenosyl-L-methionine
Binding site2391S-adenosyl-L-methionine
Binding site2591S-adenosyl-L-methionine

Amino acid modifications

Modified residue11N-acetylmethionine Ref.9

Natural variations

Alternative sequence1 – 170170Missing in isoform 2.
VSP_012416
Alternative sequence1 – 5959Missing in isoform 3.
VSP_035601
Alternative sequence171 – 1766LFEAFA → MEEEEE in isoform 2.
VSP_012417

Experimental info

Sequence conflict131K → N in BAB86333. Ref.1
Sequence conflict131K → N in AAH31010. Ref.6
Sequence conflict1401K → R in AAH31010. Ref.6

Secondary structure

........................................................................ 428
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified November 4, 2008. Version 4.
Checksum: 2079357016F200AC

FASTA42849,097
        10         20         30         40         50         60 
MEPLKVEKFA TAKRGNGLRA VTPLRPGELL FRSDPLAYTV CKGSRGVVCD RCLLGKEKLM 

        70         80         90        100        110        120 
RCSQCRVAKY CSAKCQKKAW PDHKRECKCL KSCKPRYPPD SVRLLGRVVF KLMDGAPSES 

       130        140        150        160        170        180 
EKLYSFYDLE SNINKLTEDK KEGLRQLVMT FQHFMREEIQ DASQLPPAFD LFEAFAKVIC 

       190        200        210        220        230        240 
NSFTICNAEM QEVGVGLYPS ISLLNHSCDP NCSIVFNGPH LLLRAVRDIE VGEELTICYL 

       250        260        270        280        290        300 
DMLMTSEERR KQLRDQYCFE CDCFRCQTQD KDADMLTGDE QVWKEVQESL KKIEELKAHW 

       310        320        330        340        350        360 
KWEQVLAMCQ AIISSNSERL PDINIYQLKV LDCAMDACIN LGLLEEALFY GTRTMEPYRI 

       370        380        390        400        410        420 
FFPGSHPVRG VQVMKVGKLQ LHQGMFPQAM KNLRLAFDIM RVTHGREHSL IEDLILLLEE 


CDANIRAS 

« Hide

Isoform 2 [UniParc].

Checksum: C9A509C511BA28C4
Show »

FASTA25829,759
Isoform 3 [UniParc].

Checksum: B5A3DC1D5C8AA743
Show »

FASTA36942,625

References

« Hide 'large scale' references
[1]"SMYD3 encodes a histone methyltransferase involved in the proliferation of cancer cells."
Hamamoto R., Furukawa Y., Morita M., Iimura Y., Silva F.P., Li M., Yagyu R., Nakamura Y.
Nat. Cell Biol. 6:731-740(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INTERACTION WITH HSPCA; HELZ AND POLR2A, DNA-BINDING.
[2]Sha J.H., Zhou Z.M., Xu M.
Submitted (NOV-2002) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
Tissue: Testis.
[3]"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. expand/collapse author list , 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] (ISOFORMS 1 AND 3).
[4]"The DNA sequence and biological annotation of human chromosome 1."
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. expand/collapse author list , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]"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] (ISOFORM 1).
Tissue: Colon and Melanoma.
[7]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[8]"Smyd3 regulates cancer cell phenotypes and catalyzes histone H4 lysine 5 methylation."
Van Aller G.S., Reynoird N., Barbash O., Huddleston M., Liu S., Zmoos A.F., McDevitt P., Sinnamon R., Le B., Mas G., Annan R., Sage J., Garcia B.A., Tummino P.J., Gozani O., Kruger R.G.
Epigenetics 7:340-343(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: CATALYTIC ACTIVITY, FUNCTION.
[9]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]"Crystal structure of human histone-lysine n-methyltransferase SMYD3 in complex with S-adenosyl-L-methionine."
Structural genomics consortium (SGC)
Submitted (APR-2010) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH S-ADENOSYL-L-METHIONINE AND ZINC IONS.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB057595 mRNA. Translation: BAB86333.1.
AY186742 mRNA. Translation: AAO31695.1.
AK024733 mRNA. Translation: BAB14981.1.
AK289605 mRNA. Translation: BAF82294.1.
AL512412, AL445468 Genomic DNA. Translation: CAI14744.1. Different initiation.
AL512412, AL445468 Genomic DNA. Translation: CAI14745.1.
AL512412 expand/collapse EMBL AC list , AL356583, AL358859, AL445468 Genomic DNA. Translation: CAI14746.1.
AL358859 expand/collapse EMBL AC list , AL356583, AL445468, AL512412 Genomic DNA. Translation: CAI15419.1.
AL356583 expand/collapse EMBL AC list , AL358859, AL445468, AL512412 Genomic DNA. Translation: CAI16395.1.
AL445468, AL512412 Genomic DNA. Translation: CAI16628.1. Different initiation.
AL445468, AL512412 Genomic DNA. Translation: CAI16629.1.
AL445468 expand/collapse EMBL AC list , AL356583, AL358859, AL512412 Genomic DNA. Translation: CAI16630.1.
CH471148 Genomic DNA. Translation: EAW77142.1.
BC017079 mRNA. Translation: AAH17079.2.
BC031010 mRNA. Translation: AAH31010.1.
CCDSCCDS31083.1. [Q9H7B4-3]
CCDS53486.1. [Q9H7B4-1]
RefSeqNP_001161212.1. NM_001167740.1. [Q9H7B4-1]
NP_073580.1. NM_022743.2. [Q9H7B4-3]
XP_005273286.1. XM_005273229.1. [Q9H7B4-2]
UniGeneHs.567571.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3MEKX-ray2.10A1-428[»]
3OXFX-ray2.82A/B1-428[»]
3OXGX-ray3.41A1-428[»]
3OXLX-ray3.60A1-428[»]
3PDNX-ray1.70A1-428[»]
3QWPX-ray1.53A1-428[»]
3RU0X-ray1.85A/B2-428[»]
ProteinModelPortalQ9H7B4.
SMRQ9H7B4. Positions 4-428.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid122268. 22 interactions.
IntActQ9H7B4. 11 interactions.
MINTMINT-1033215.
STRING9606.ENSP00000373637.

Chemistry

ChEMBLCHEMBL2321643.

PTM databases

PhosphoSiteQ9H7B4.

Polymorphism databases

DMDM212276523.

Proteomic databases

MaxQBQ9H7B4.
PaxDbQ9H7B4.
PRIDEQ9H7B4.

Protocols and materials databases

DNASU64754.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000388985; ENSP00000373637; ENSG00000185420. [Q9H7B4-1]
ENST00000490107; ENSP00000419184; ENSG00000185420. [Q9H7B4-3]
ENST00000541742; ENSP00000444184; ENSG00000185420. [Q9H7B4-3]
GeneID64754.
KEGGhsa:64754.
UCSCuc001ibj.3. human. [Q9H7B4-1]

Organism-specific databases

CTD64754.
GeneCardsGC01M245912.
HGNCHGNC:15513. SMYD3.
HPACAB012229.
MIM608783. gene.
neXtProtNX_Q9H7B4.
PharmGKBPA37972.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG2940.
HOGENOMHOG000007850.
HOVERGENHBG105004.
InParanoidQ9H7B4.
KOK11426.
OMAKVEKFAT.
OrthoDBEOG74XS68.
PhylomeDBQ9H7B4.
TreeFamTF106487.

Gene expression databases

ArrayExpressQ9H7B4.
BgeeQ9H7B4.
CleanExHS_SMYD3.
GenevestigatorQ9H7B4.

Family and domain databases

InterProIPR025805. Hist-Lys_N-MeTrfase_Smyd3.
IPR001214. SET_dom.
IPR002893. Znf_MYND.
[Graphical view]
PfamPF00856. SET. 1 hit.
PF01753. zf-MYND. 1 hit.
[Graphical view]
SMARTSM00317. SET. 1 hit.
[Graphical view]
PROSITEPS51574. SAM_MT43_2. 1 hit.
PS50280. SET. 1 hit.
PS01360. ZF_MYND_1. 1 hit.
PS50865. ZF_MYND_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSSMYD3. human.
EvolutionaryTraceQ9H7B4.
GeneWikiSMYD3.
GenomeRNAi64754.
NextBio66717.
PROQ9H7B4.
SOURCESearch...

Entry information

Entry nameSMYD3_HUMAN
AccessionPrimary (citable) accession number: Q9H7B4
Secondary accession number(s): A8K0P0 expand/collapse secondary AC list , B1AN38, Q86TL8, Q8N5Z6, Q96AI5
Entry history
Integrated into UniProtKB/Swiss-Prot: May 16, 2003
Last sequence update: November 4, 2008
Last modified: July 9, 2014
This is version 118 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM