Reviewed, UniProtKB/Swiss-Prot O60016 (CLR4_SCHPO)

Names and origin

Protein names

Recommended name:
    Histone-lysine N-methyltransferase, H3 lysine-9 specific
    EC=2.1.1.43
Alternative name(s):
    Histone H3-K9 methyltransferase
    H3-K9-HMTase
    Cryptic loci regulator 4
    Lysine N-methyltransferase 1

Gene names

Name:	clr4
Synonyms:	kmt1
ORF Names:	SPBC428.08c

Organism

Schizosaccharomyces pombe (Fission yeast) [Complete proteome]

Taxonomic identifier

4896 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Taphrinomycotina › Schizosaccharomycetes › Schizosaccharomycetales › Schizosaccharomycetaceae › Schizosaccharomyces

Protein attributes

Sequence length	490 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Histone methyltransferase. Catalytic component of the rik1-associated E3 ubiquitin ligase complex that shows ubiquitin ligase activity and is required for histone H3K9 methylation. H3K9me represents a specific tag for epigenetic transcriptional repression by recruiting swi6/HP1 to methylated histones which leads to transcriptional silencing within centromeric heterochromatin, telomeric regions and at the silent mating-type loci. Ref.4 Ref.6
Catalytic activity	S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N(6)-methyl-L-lysine. Ref.7
Subunit structure	Component of the rik1-associated E3 ubiquitin ligase complex composed of at least clr4, cul4, pip1, raf1 and raf2. Interacts directly with cul4. Ref.5
Subcellular location	Nucleus. Cytoplasm › cytoskeleton › spindle pole body. Ref.8
Sequence similarities	Belongs to the histone-lysine methyltransferase family. Suvar3-9 subfamily. Contains 1 chromo domain. Contains 1 post-SET domain. Contains 1 pre-SET domain. Contains 1 SET domain.

Ontologies

Keywords
Cellular component	Cytoplasm Cytoskeleton Nucleus
Ligand	Metal-binding S-adenosyl-L-methionine Zinc
Molecular function	Chromatin regulator Methyltransferase Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	attachment of spindle microtubules to kinetochore during mitosis Inferred from mutant phenotype. Source: GeneDB_SPombe cellular protein localization Ref.7 Inferred from genetic interaction. Source: GeneDB_SPombe chromatin assembly or disassembly Inferred from electronic annotation. Source: InterPro chromatin silencing at centromere Inferred from mutant phenotype. Source: GeneDB_SPombe chromatin silencing at rDNA Inferred from mutant phenotype. Source: GeneDB_SPombe chromatin silencing at silent mating-type cassette Ref.6 Inferred from mutant phenotype. Source: GeneDB_SPombe chromatin silencing at telomere Traceable author statement. Source: GeneDB_SPombe donor selection Ref.1 Inferred from mutant phenotype. Source: GeneDB_SPombe histone methylation Inferred from direct assay. Source: GeneDB_SPombe horsetail nuclear movement Inferred from genetic interaction. Source: GeneDB_SPombe meiotic telomere clustering Inferred from mutant phenotype. Source: GeneDB_SPombe production of siRNA involved in RNA interference Inferred from mutant phenotype. Source: GeneDB_SPombe
Cellular component	Rik1-E3 ubiquitin ligase complex Ref.5 Inferred from direct assay. Source: GeneDB_SPombe mating-type region heterochromatin Non-traceable author statement. Source: GeneDB_SPombe nuclear centromeric heterochromatin Ref.5 Traceable author statement. Source: GeneDB_SPombe nuclear telomeric heterochromatin Non-traceable author statement. Source: GeneDB_SPombe spindle pole body Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	chromatin binding Inferred from electronic annotation. Source: InterPro histone methyltransferase activity (H3-K9 specific) Inferred from direct assay. Source: UniProtKB protein binding Ref.4 Ref.5 Inferred from physical interaction. Source: IntAct zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
	P68432	1	EBI-354657,EBI-79764	From a different organism.
cul4	O14122	3	EBI-354657,EBI-904890
rik1	Q10426	2	EBI-354657,EBI-1111936

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 490

490

Histone-lysine N-methyltransferase, H3 lysine-9 specific

PRO_0000186063

Regions

Domain

8 – 69

62

Chromo

Domain

258 – 325

68

Pre-SET

Domain

327 – 456

130

SET

Domain

473 – 489

17

Post-SET

Region

338 – 340

3

S-adenosyl-L-methionine binding By similarity

Region

409 – 410

2

S-adenosyl-L-methionine binding By similarity

Sites

Metal binding

260

1

Zinc 1

Metal binding

262

1

Zinc 1

Metal binding

268

1

Zinc 2

Metal binding

276

1

Zinc 1

Metal binding

278

1

Zinc 3

Metal binding

307

1

Zinc 2

Metal binding

307

1

Zinc 3

Metal binding

311

1

Zinc 3

Metal binding

313

1

Zinc 2

Metal binding

317

1

Zinc 2

Metal binding

412

1

Zinc 4 By similarity

Metal binding

477

1

Zinc 4 By similarity

Metal binding

479

1

Zinc 4 By similarity

Metal binding

484

1

Zinc 4 By similarity

Binding site

381

1

S-adenosyl-L-methionine By similarity

Experimental info

Mutagenesis

31

1

W → G: Weak effect on methyltransferase activity. Ref.7

Mutagenesis

41

1

W → G: Weak effect on methyltransferase activity. Ref.7

Mutagenesis

320

1

R → H: Abolishes methyltransferase activity. Ref.7

Mutagenesis

378

1

G → S: Abolishes methyltransferase activity. Ref.7

Mutagenesis

486

1

G → D: Abolishes methyltransferase activity. Ref.7

Sequence conflict

19

1

D → G in AAC18302. Ref.1

Sequence conflict

142

1

Missing AA sequence Ref.4

Sequence conflict

437

1

A → G in AAC18302. Ref.1

Secondary structure

1

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490

Helix Strand Turn

Details...

Helix

196 – 214

19

Beta strand

216 – 219

4

Beta strand

221 – 224

4

Beta strand

237 – 239

3

Helix

254 – 256

3

Beta strand

265 – 268

4

Turn

273 – 275

3

Beta strand

277 – 279

3

Beta strand

294 – 296

3

Beta strand

302 – 305

4

Helix

322 – 324

3

Beta strand

330 – 334

5

Beta strand

336 – 346

11

Beta strand

353 – 356

4

Beta strand

360 – 363

4

Helix

364 – 371

8

Beta strand

382 – 385

4

Beta strand

390 – 392

3

Beta strand

394 – 397

4

Beta strand

399 – 402

4

Helix

404 – 407

4

Beta strand

415 – 423

9

Beta strand

432 – 439

8

Beta strand

455 – 458

4

Sequences

	Sequence		Length	Mass (Da)
	O60016-1 [UniParc]. Last modified December 8, 2000. Version 2. Checksum: 53C3EC87BCBA51FF	FASTA	490	55,918
	10 20 30 40 50 60 MSPKQEEYEV ERIVDEKLDR NGAVKLYRIR WLNYSSRSDT WEPPENLSGC SAVLAEWKRR 70 80 90 100 110 120 KRRLKGSNSD SDSPHHASNP HPNSRQKHQH QTSKSVPRSQ RFSRELNVKK ENKKVFSSQT 130 140 150 160 170 180 TKRQSRKQST ALTTNDTSII LDDSLHTNSK KLGKTRNEVK EESQKRELVS NSIKEATSPK 190 200 210 220 230 240 TSSILTKPRN PSKLDSYTHL SFYEKRELFR KKLREIEGPE VTLVNEVDDE PCPSLDFQFI 250 260 270 280 290 300 SQYRLTQGVI PPDPNFQSGC NCSSLGGCDL NNPSRCECLD DLDEPTHFAY DAQGRVRADT 310 320 330 340 350 360 GAVIYECNSF CSCSMECPNR VVQRGRTLPL EIFKTKEKGW GVRSLRFAPA GTFITCYLGE 370 380 390 400 410 420 VITSAEAAKR DKNYDDDGIT YLFDLDMFDD ASEYTVDAQN YGDVSRFFNH SCSPNIAIYS 430 440 450 460 470 480 AVRNHGFRTI YDLAFFAIKD IQPLEELTFD YAGAKDFSPV QSQKSQQNRI SKLRRQCKCG 490 SANCRGWLFG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The chromo and SET domains of the Clr4 protein are essential for silencing in fission yeast." Ivanova A.V., Bonaduce M.J., Ivanov S.V., Klar A.J.S. Nat. Genet. 19:192-195(1998) [PubMed: 9620780] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	Lord P. Thesis (1998), University of Edinburgh, United Kingdom Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: SP813.
[3]	"The genome sequence of Schizosaccharomyces pombe." Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M. , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P. Nature 415:871-880(2002) [PubMed: 11859360] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 38366 / 972.
[4]	"A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation." Horn P.J., Bastie J.-N., Peterson C.L. Genes Dev. 19:1705-1714(2005) [PubMed: 16024659] [Abstract] Cited for: PARTIAL PROTEIN SEQUENCE, IDENTIFICATION IN THE RIK1-ASSOCIATED E3 UBIQUITIN LIGASE COMPLEX, FUNCTION.
[5]	"Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin." Jia S., Kobayashi R., Grewal S.I.S. Nat. Cell Biol. 7:1007-1013(2005) [PubMed: 16127433] [Abstract] Cited for: PROTEIN SEQUENCE OF 64-85; 127-150; 190-205; 371-406; 429-455 AND 486-490, INTERACTION WITH CUL4.
[6]	"Mutations in rik1, clr2, clr3 and clr4 genes asymmetrically derepress the silent mating-type loci in fission yeast." Ekwall K., Ruusala T. Genetics 136:53-64(1994) [PubMed: 8138176] [Abstract] Cited for: FUNCTION.
[7]	"Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly." Nakayama J., Rice J.C., Strahl B.D., Allis C.D., Grewal S.I.S. Science 292:110-113(2001) [PubMed: 11283354] [Abstract] Cited for: ENZYME ACTIVITY, MUTAGENESIS OF TRP-31; TRP-41; ARG-320; GLY-378 AND GLY-486.
[8]	"ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe." Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S., Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S., Yoshida M. Nat. Biotechnol. 24:841-847(2006) [PubMed: 16823372] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[9]	"Solution structure, domain features, and structural implications of mutants of the chromo domain from the fission yeast histone methyltransferase Clr4." Horita D.A., Ivanova A.V., Altieri A.S., Klar A.J., Byrd R.A. J. Mol. Biol. 307:861-870(2001) [PubMed: 11273706] [Abstract] Cited for: STRUCTURE BY NMR OF 2-69.
[10]	"Structure of the SET domain histone lysine methyltransferase Clr4." Min J., Zhang X., Cheng X., Grewal S.I.S., Xu R.M. Nat. Struct. Biol. 9:828-832(2002) [PubMed: 12389037] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 192-490 IN COMPLEX WITH ZINC IONS.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AF061854 Genomic DNA. Translation: AAC18302.1.
AJ007840 Genomic DNA. Translation: CAA07709.1.
CU329671 Genomic DNA. Translation: CAA22283.1.

PIR

T43700.
T43745.

RefSeq

NP_595186.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1G6Z	NMR	-	A	2-69	[»]
1MVH	X-ray	2.30	A	192-490	[»]
1MVX	X-ray	3.00	A	192-490	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

O60016. 3 interactions.

STRING

O60016.

Genome annotation databases

GeneID

2540825.

GenomeReviews

Gene locus clr4 in contig CU329671_GR.

KEGG

spo:SPBC428.08c.

NMPDR

fig|4896.1.peg.1052.

Organism-specific databases

GeneDB_Spombe

SPBC428.08c.

Enzyme and pathway databases

BioCyc

SPOM-XXX-01:SPOM-XXX-01-003278-MON.

BRENDA

2.1.1.43. 653.

Gene expression databases

ArrayExpress

O60016.

Family and domain databases

InterPro

IPR000953. Chromodomain.
IPR003616. Post-SET_Zn_bd.
IPR007728. Pre-SET_Zn_bd.
IPR003606. Pre-SET_Zn_bd_sub.
IPR001214. SET.
[Graphical view]

Pfam

PF00385. Chromo. 1 hit.
PF05033. Pre-SET. 1 hit.
PF00856. SET. 1 hit.
[Graphical view]

SMART

SM00298. CHROMO. 1 hit.
SM00508. PostSET. 1 hit.
SM00468. PreSET. 1 hit.
SM00317. SET. 1 hit.
[Graphical view]

PROSITE

PS00598. CHROMO_1. 1 hit.
PS50013. CHROMO_2. 1 hit.
PS50868. POST_SET. 1 hit.
PS50867. PRE_SET. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

CLR4_SCHPO

Accession

Primary (citable) accession number: O60016
Secondary accession number(s): O74565

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 8, 2000
Last sequence update:	December 8, 2000
Last modified:	October 13, 2009
This is version 98 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)