Reviewed, UniProtKB/Swiss-Prot Q9NQR1 (SETD8_HUMAN)

Names and origin

Protein names

Recommended name:
    Histone-lysine N-methyltransferase SETD8
    EC=2.1.1.43
Alternative name(s):
    H4-K20-HMTase SETD8
    SET domain-containing protein 8
    PR/SET domain-containing protein 07
      Short name=PR/SET07
      Short name=PR-Set7
    Lysine N-methyltransferase 5A

Gene names

Name:	SETD8
Synonyms:	KMT5A, PRSET7, SET07, SET8

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	393 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Histone methyltransferase that specifically monomethylates 'Lys-20' of histone H4. H4 'Lys-20' monomethylation is enriched during mitosis and represents a specific tag for epigenetic transcriptional repression. Mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. Required for cell proliferation, probably by contributing to the maintenance of proper higher order structure of DNA during mitosis. Involved in chromosome condensation and proper cytokinesis. Nucleosomes are preferred as substrate compared to free histones. Ref.7 Ref.9 Ref.11 Ref.12
Catalytic activity	S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N(6)-methyl-L-lysine. Ref.8
Subcellular location	Nucleus. Note: Specifically localizes to mitotic chromosomes. Associates with silent chromatin on euchromatic arms. Not associated with constitutive heterochromatin. Ref.6
Developmental stage	Not detected during G1 phase. First detected during S through G2 phases, and peaks during mitosis (at protein level). Ref.6
Induction	By HCFC1 C-terminal chain, independently of HCFC1 N-terminal chain. Ref.7
Domain	Although the SET domain contains the active site of enzymatic activity, both sequences upstream and downstream of the SET domain are required for methyltransferase activity.
Sequence similarities	Belongs to the histone-lysine methyltransferase family. PR/SET subfamily. Contains 1 SET domain.
Caution	It is uncertain whether Met-1 or Met-72 is the initiator.

Ontologies

Keywords
Biological process	Cell cycle Cell division Mitosis Transcription Transcription regulation
Cellular component	Chromosomal protein Nucleus
Coding sequence diversity	Alternative splicing
Domain	Coiled coil
Ligand	S-adenosyl-L-methionine
Molecular function	Chromatin regulator Methyltransferase Repressor Transferase
PTM	Phosphoprotein
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	cell division Inferred from electronic annotation. Source: UniProtKB-KW chromatin modification Inferred from electronic annotation. Source: UniProtKB-KW mitosis Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	chromosome Inferred from electronic annotation. Source: UniProtKB-KW nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	histone-lysine N-methyltransferase activity Inferred from electronic annotation. Source: EC protein binding Ref.11 Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
HIST1H4A	P62805	4	EBI-1268946,EBI-302023

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q9NQR1-1)

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: Q9NQR1-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-41: Missing.
     42-57: PGRAAGGKMSKPCAVE → MARGRKMSKPRAVEAA

Note: No experimental confirmation available.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 393

393

Histone-lysine N-methyltransferase SETD8

PRO_0000186081

Regions

Domain

256 – 382

127

SET

Region

267 – 269

3

S-adenosyl-L-methionine binding

Region

339 – 340

2

S-adenosyl-L-methionine binding

Coiled coil

134 – 163

30

Potential

Compositional bias

6 – 67

62

Ala-rich

Compositional bias

29 – 32

4

Poly-Arg

Sites

Binding site

312

1

S-adenosyl-L-methionine

Amino acid modifications

Modified residue

100

1

Phosphoserine Ref.10

Natural variations

Alternative sequence

1 – 41

41

Missing in isoform 2.

VSP_002226

Alternative sequence

42 – 57

16

PGRAA…PCAVE → MARGRKMSKPRAVEAA in isoform 2.

VSP_002227

Experimental info

Mutagenesis

286

1

Y → A or F: Strongly reduces affinity for histone H4 and abolishes methyltransferase activity. Ref.12

Mutagenesis

300

1

E → A: Strongly reduces affinity for histone H4. Ref.12

Mutagenesis

311

1

C → A: Strongly reduces affinity for histone H4. Ref.12

Mutagenesis

336

1

R → G: Abolishes methyltransferase activity. Ref.1

Mutagenesis

340

1

H → A: Strongly decreases methyltransferase activity. Ref.2

Mutagenesis

375

1

Y → A: Strongly reduces affinity for histone H4 and methyltransferase activity. Ref.12

Mutagenesis

375

1

Y → F: Alters methyltransferase activity, so that both monomethylation and dimethylation take place. Ref.12

Mutagenesis

379

1

D → A or N: Abolishes histone H4 binding and methyltransferase activity. Ref.12

Mutagenesis

385 – 393

9

Missing: Abolishes methyltransferase activity. Ref.2

Mutagenesis

388

1

H → A or E: Strongly reduces affinity for histone H4. Ref.12

Mutagenesis

388

1

H → F: Increases affinity for histone H4. Ref.12

Sequence conflict

162 – 163

2

KG → RR in AAF97812. Ref.3

Sequence conflict

281

1

D → A in AAF97812. Ref.3

Sequence conflict

343

1

C → R in AAF97812. Ref.3

Sequence conflict

357

1

P → R in AAH50346. Ref.5

Sequence conflict

373

1

L → P in AAF97812. Ref.3

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

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.

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393

Helix Strand Turn

Details...

Helix

236 – 253

18

Beta strand

259 – 264

6

Turn

265 – 267

3

Beta strand

268 – 275

8

Beta strand

282 – 286

5

Beta strand

288 – 292

5

Helix

293 – 303

11

Beta strand

313 – 318

6

Beta strand

321 – 326

6

Helix

335 – 337

3

Beta strand

345 – 353

9

Beta strand

356 – 365

10

Helix

382 – 387

6

Helix

389 – 392

4

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified November 15, 2002. Version 3. Checksum: 2DCD9B697834B5BD	FASTA	393	42,890
	10 20 30 40 50 60 MGEGGAAAAL VAAAAAAAAA AAAVVAGQRR RRLGRRARCH GPGRAAGGKM SKPCAVEAAA 70 80 90 100 110 120 AAVAATAPGP EMVERRGPGR PRTDGENVFT GQSKIYSYMS PNKCSGMRFP LQEENSVTHH 130 140 150 160 170 180 EVKCQGKPLA GIYRKREEKR NAGNAVRSAM KSEEQKIKDA RKGPLVPFPN QKSEAAEPPK 190 200 210 220 230 240 TPPSSCDSTN AAIAKQALKK PIKGKQAPRK KAQGKTQQNR KLTDFYPVRR SSRKSKAELQ 250 260 270 280 290 300 SEERKRIDEL IESGKEEGMK IDLIDGKGRG VIATKQFSRG DFVVEYHGDL IEITDAKKRE 310 320 330 340 350 360 ALYAQDPSTG CYMYYFQYLS KTYCVDATRE TNRLGRLINH SKCGNCQTKL HDIDGVPHLI 370 380 390 LIASRDIAAG EELLYDYGDR SKASIEAHPW LKH
	Isoform 2. Checksum: E0DA1AB9881EE4E6	FASTA	352	39,223
	10 20 30 40 50 60 MARGRKMSKP RAVEAAAAAA AVAATAPGPE MVERRGPGRP RTDGENVFTG QSKIYSYMSP 70 80 90 100 110 120 NKCSGMRFPL QEENSVTHHE VKCQGKPLAG IYRKREEKRN AGNAVRSAMK SEEQKIKDAR 130 140 150 160 170 180 KGPLVPFPNQ KSEAAEPPKT PPSSCDSTNA AIAKQALKKP IKGKQAPRKK AQGKTQQNRK 190 200 210 220 230 240 LTDFYPVRRS SRKSKAELQS EERKRIDELI ESGKEEGMKI DLIDGKGRGV IATKQFSRGD 250 260 270 280 290 300 FVVEYHGDLI EITDAKKREA LYAQDPSTGC YMYYFQYLSK TYCVDATRET NRLGRLINHS 310 320 330 340 350 KCGNCQTKLH DIDGVPHLIL IASRDIAAGE ELLYDYGDRS KASIEAHPWL KH

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin." Nishioka K., Rice J.C., Sarma K., Erdjument-Bromage H., Werner J., Wang Y., Chuikov S., Valenzuela P., Tempst P., Steward R., Lis J.T., Allis C.D., Reinberg D. Mol. Cell 9:1201-1213(2002) [PubMed: 12086618] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), PROTEIN SEQUENCE OF 108-131; 220-231 AND 349-393, CHARACTERIZATION, MUTAGENESIS OF ARG-336. Tissue: Cervix carcinoma.
[2]	"Purification and functional characterization of SET8, a nucleosomal histone H4-lysine 20-specific methyltransferase." Fang J., Feng Q., Ketel C.S., Wang H., Cao R., Xia L., Erdjument-Bromage H., Tempst P., Simon J.A., Zhang Y. Curr. Biol. 12:1086-1099(2002) [PubMed: 12121615] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), PROTEIN SEQUENCE OF 83-103; 109-134; 141-151; 162-172; 221-230; 245-260; 280-297 AND 350-393, CHARACTERIZATION, MUTAGENESIS OF HIS-340 AND 385-ILE--HIS-393.
[3]	"A novel PR/SET domain-containing gene, SET07, as a candidate tumor suppressor." Tain F., Huang S. Submitted (JUL-2001) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[4]	"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: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). Tissue: Thymus.
[5]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). Tissue: Testis.
[6]	"Mitotic-specific methylation of histone H4 Lys 20 follows increased PR-Set7 expression and its localization to mitotic chromosomes." Rice J.C., Nishioka K., Sarma K., Steward R., Reinberg D., Allis C.D. Genes Dev. 16:2225-2230(2002) [PubMed: 12208845] [Abstract] Cited for: SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE.
[7]	"A switch in mitotic histone H4 lysine 20 methylation status is linked to M phase defects upon loss of HCF-1." Julien E., Herr W. Mol. Cell 14:713-725(2004) [PubMed: 15200950] [Abstract] Cited for: FUNCTION, INDUCTION.
[8]	"SET8 recognizes the sequence RHRK20VLRDN within the N terminus of histone H4 and mono-methylates lysine 20." Yin Y., Liu C., Tsai S.N., Zhou B., Ngai S.M., Zhu G. J. Biol. Chem. 280:30025-30031(2005) [PubMed: 15964846] [Abstract] Cited for: CATALYTIC ACTIVITY.
[9]	"A trans-tail histone code defined by monomethylated H4 Lys-20 and H3 Lys-9 demarcates distinct regions of silent chromatin." Sims J.K., Houston S.I., Magazinnik T., Rice J.C. J. Biol. Chem. 281:12760-12766(2006) [PubMed: 16517599] [Abstract] Cited for: FUNCTION.
[10]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-100, MASS SPECTROMETRY.
[11]	"Specificity and mechanism of the histone methyltransferase Pr-Set7." Xiao B., Jing C., Kelly G., Walker P.A., Muskett F.W., Frenkiel T.A., Martin S.R., Sarma K., Reinberg D., Gamblin S.J., Wilson J.R. Genes Dev. 19:1444-1454(2005) [PubMed: 15933069] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 233-393 IN COMPLEX WITH HISTONE H4 AND S-ADENOSYLMETHIONINE, FUNCTION.
[12]	"Structural and functional analysis of SET8, a histone H4 'Lys-20' methyltransferase." Couture J.-F., Collazo E., Brunzelle J.S., Trievel R.C. Genes Dev. 19:1455-1465(2005) [PubMed: 15933070] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) OF 231-393 IN COMPLEX WITH HISTONE H4 AND S-ADENOSYLMETHIONINE, FUNCTION, MUTAGENESIS OF TYR-286; GLU-300; CYS-311; TYR-375; ASP-379 AND HIS-388.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AY064546 mRNA. Translation: AAL40879.1. Different initiation.
AY102937 mRNA. Translation: AAM47033.1.
AF287261 mRNA. Translation: AAF97812.2.
AK292645 mRNA. Translation: BAF85334.1.
BC050346 mRNA. Translation: AAH50346.1.

IPI

IPI00288890.
IPI00375894.

RefSeq

NP_065115.3.

UniGene

Hs.443735
Hs.572262

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ZKK	X-ray	1.45	A/B/C/D	231-393	[»]
2BQZ	X-ray	1.50	A/E	233-393	[»]
3F9W	X-ray	1.60	A/B/C/D	232-393	[»]
3F9X	X-ray	1.25	A/B/C/D	232-393	[»]
3F9Y	X-ray	1.50	A/B	232-393	[»]
3F9Z	X-ray	1.60	A/B/C/D	232-393	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

Q9NQR1. 1 interaction.

PTM databases

PhosphoSite

Q9NQR1.

Proteomic databases

PRIDE

Q9NQR1.

Genome annotation databases

Ensembl

ENSG00000183955. Homo sapiens. [Contig view]

GeneID

387893.

KEGG

hsa:387893.

Organism-specific databases

GeneCards

GC02M091298.
GC12P122434.
GC12P122435.

H-InvDB

HIX0020766.
HIX0026375.
HIX0030601.
HIX0037637.

HGNC

HGNC:29489. SETD8.

MIM

607240. gene.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

Q9NQR1.

HOVERGEN

Q9NQR1.

OMA

Q9NQR1. FSRGEFV.

Enzyme and pathway databases

BRENDA

2.1.1.43. 247.

Gene expression databases

Bgee

Q9NQR1.

CleanEx

HS_SETD8.

Family and domain databases

InterPro

IPR016858. Hist_H4-K20_MeTrfase.
IPR001214. SET.
[Graphical view]

Pfam

PF00856. SET. 1 hit.
[Graphical view]

PIRSF

PIRSF027717. Histone_H4-K20_mtfrase. 1 hit.

SMART

SM00317. SET. 1 hit.
[Graphical view]

PROSITE

PS50280. SET. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

101711.

SOURCE

Search...

Entry information

Entry name

SETD8_HUMAN

Accession

Primary (citable) accession number: Q9NQR1
Secondary accession number(s): A8K9D0, Q86W83, Q8TD09

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 15, 2002
Last sequence update:	November 15, 2002
Last modified:	June 16, 2009
This is version 78 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)