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Protein

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

Gene

clr4

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.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
Metal bindingi260Zinc 11
Metal bindingi260Zinc 21
Metal bindingi262Zinc 11
Metal bindingi268Zinc 11
Metal bindingi268Zinc 31
Metal bindingi276Zinc 11
Metal bindingi278Zinc 21
Metal bindingi307Zinc 21
Metal bindingi307Zinc 31
Metal bindingi311Zinc 21
Metal bindingi313Zinc 31
Metal bindingi317Zinc 31
Binding sitei381S-adenosyl-L-methioninePROSITE-ProRule annotation1
Binding sitei406S-adenosyl-L-methioninePROSITE-ProRule annotation1
Metal bindingi412Zinc 4By similarity1
Metal bindingi477Zinc 4By similarity1
Metal bindingi479Zinc 4By similarity1
Metal bindingi484Zinc 4By similarity1

GO - Molecular functioni

  • double-stranded DNA binding Source: PomBase
  • histone methyltransferase activity Source: PomBase
  • histone methyltransferase activity (H3-K9 specific) Source: UniProtKB
  • methylated histone binding Source: PomBase
  • methyltransferase activity Source: UniProtKB
  • single-stranded DNA binding Source: PomBase
  • single-stranded RNA binding Source: PomBase
  • zinc ion binding Source: InterPro

GO - Biological processi

  • cellular protein localization Source: PomBase
  • chromatin remodeling Source: PomBase
  • chromatin silencing at centromere Source: PomBase
  • chromatin silencing at centromere outer repeat region Source: PomBase
  • chromatin silencing at rDNA Source: PomBase
  • chromatin silencing at silent mating-type cassette Source: PomBase
  • chromatin silencing at telomere Source: PomBase
  • chromatin silencing by small RNA Source: PomBase
  • donor selection Source: PomBase
  • heterochromatin maintenance involved in chromatin silencing at centromere outer repeat region Source: PomBase
  • histone H3-K9 methylation Source: PomBase
  • meiotic telomere clustering Source: PomBase
  • negative regulation of transcription from RNA polymerase II promoter Source: PomBase
  • regulation of production of siRNA involved in RNA interference Source: PomBase
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Methyltransferase, Transferase

Keywords - Ligandi

Metal-binding, S-adenosyl-L-methionine, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Histone-lysine N-methyltransferase, H3 lysine-9 specific (EC:2.1.1.43)
Alternative name(s):
Cryptic loci regulator 4
Histone H3-K9 methyltransferase
Short name:
H3-K9-HMTase
Lysine N-methyltransferase 1
Gene namesi
Name:clr4
Synonyms:kmt1
ORF Names:SPBC428.08c
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:SPBC428.08c.
PomBaseiSPBC428.08c. clr4.

Subcellular locationi

GO - Cellular componenti

  • chromosome, centromeric outer repeat region Source: GOC
  • chromosome, telomeric region Source: GOC
  • CLRC ubiquitin ligase complex Source: PomBase
  • cytoplasm Source: UniProtKB-KW
  • mitotic spindle pole body Source: PomBase
  • nuclear pericentric heterochromatin Source: PomBase
  • nucleus Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Cytoplasm, Cytoskeleton, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi31W → G: Weak effect on methyltransferase activity. 1 Publication1
Mutagenesisi41W → G: Weak effect on methyltransferase activity. 1 Publication1
Mutagenesisi320R → H: Abolishes methyltransferase activity. 1 Publication1
Mutagenesisi378G → S: Abolishes methyltransferase activity. 1 Publication1
Mutagenesisi486G → D: Abolishes methyltransferase activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001860631 – 490Histone-lysine N-methyltransferase, H3 lysine-9 specificAdd BLAST490

Proteomic databases

MaxQBiO60016.
PRIDEiO60016.

Interactioni

Subunit structurei

Component of the rik1-associated E3 ubiquitin ligase complex composed of at least clr4, cul4, pip1, raf1 and raf2. Interacts directly with cul4.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
cul4O141223EBI-354657,EBI-904890
rik1Q104263EBI-354657,EBI-1111936
SPBP8B7.28cO942762EBI-354657,EBI-2651917

GO - Molecular functioni

  • methylated histone binding Source: PomBase

Protein-protein interaction databases

BioGridi277343. 291 interactors.
DIPiDIP-32588N.
IntActiO60016. 5 interactors.
MINTiMINT-195370.

Structurei

Secondary structure

1490
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi14 – 17Combined sources4
Beta strandi26 – 29Combined sources4
Turni32 – 35Combined sources4
Beta strandi40 – 42Combined sources3
Helixi44 – 47Combined sources4
Helixi51 – 61Combined sources11
Turni62 – 65Combined sources4
Helixi196 – 214Combined sources19
Beta strandi216 – 219Combined sources4
Beta strandi221 – 224Combined sources4
Beta strandi226 – 228Combined sources3
Beta strandi237 – 239Combined sources3
Helixi254 – 256Combined sources3
Beta strandi265 – 268Combined sources4
Turni273 – 275Combined sources3
Beta strandi277 – 279Combined sources3
Beta strandi294 – 296Combined sources3
Beta strandi302 – 305Combined sources4
Beta strandi311 – 313Combined sources3
Helixi322 – 324Combined sources3
Beta strandi330 – 334Combined sources5
Beta strandi336 – 346Combined sources11
Beta strandi353 – 356Combined sources4
Beta strandi360 – 363Combined sources4
Helixi364 – 371Combined sources8
Beta strandi382 – 385Combined sources4
Beta strandi390 – 392Combined sources3
Beta strandi394 – 397Combined sources4
Beta strandi399 – 402Combined sources4
Helixi404 – 407Combined sources4
Beta strandi415 – 423Combined sources9
Beta strandi432 – 439Combined sources8
Beta strandi455 – 458Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1G6ZNMR-A2-69[»]
1MVHX-ray2.30A192-490[»]
1MVXX-ray3.00A192-490[»]
ProteinModelPortaliO60016.
SMRiO60016.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO60016.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini8 – 69ChromoPROSITE-ProRule annotationAdd BLAST62
Domaini258 – 325Pre-SETPROSITE-ProRule annotationAdd BLAST68
Domaini328 – 452SETPROSITE-ProRule annotationAdd BLAST125
Domaini473 – 489Post-SETPROSITE-ProRule annotationAdd BLAST17

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni338 – 340S-adenosyl-L-methionine bindingBy similarity3
Regioni409 – 410S-adenosyl-L-methionine bindingBy similarity2

Domaini

In the pre-SET domain, Cys residues bind 3 zinc ions that are arranged in a triangular cluster; some of these Cys residues contribute to the binding of two zinc ions within the cluster.

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. Suvar3-9 subfamily.PROSITE-ProRule annotation
Contains 1 chromo domain.PROSITE-ProRule annotation
Contains 1 post-SET domain.PROSITE-ProRule annotation
Contains 1 pre-SET domain.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Phylogenomic databases

InParanoidiO60016.
KOiK11419.
OrthoDBiEOG092C2EWO.
PhylomeDBiO60016.

Family and domain databases

InterProiIPR000953. Chromo/shadow_dom.
IPR023780. Chromo_domain.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
IPR011381. Histone_H3-K9_MeTrfase.
IPR003616. Post-SET_dom.
IPR007728. Pre-SET_dom.
IPR001214. SET_dom.
[Graphical view]
PfamiPF00385. Chromo. 1 hit.
PF05033. Pre-SET. 1 hit.
PF00856. SET. 1 hit.
[Graphical view]
PIRSFiPIRSF009343. SUV39_SET. 1 hit.
SMARTiSM00298. CHROMO. 1 hit.
SM00508. PostSET. 1 hit.
SM00468. PreSET. 1 hit.
SM00317. SET. 1 hit.
[Graphical view]
SUPFAMiSSF54160. SSF54160. 1 hit.
PROSITEiPS00598. 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]

Sequencei

Sequence statusi: Complete.

O60016-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSPKQEEYEV ERIVDEKLDR NGAVKLYRIR WLNYSSRSDT WEPPENLSGC
60 70 80 90 100
SAVLAEWKRR KRRLKGSNSD SDSPHHASNP HPNSRQKHQH QTSKSVPRSQ
110 120 130 140 150
RFSRELNVKK ENKKVFSSQT TKRQSRKQST ALTTNDTSII LDDSLHTNSK
160 170 180 190 200
KLGKTRNEVK EESQKRELVS NSIKEATSPK TSSILTKPRN PSKLDSYTHL
210 220 230 240 250
SFYEKRELFR KKLREIEGPE VTLVNEVDDE PCPSLDFQFI SQYRLTQGVI
260 270 280 290 300
PPDPNFQSGC NCSSLGGCDL NNPSRCECLD DLDEPTHFAY DAQGRVRADT
310 320 330 340 350
GAVIYECNSF CSCSMECPNR VVQRGRTLPL EIFKTKEKGW GVRSLRFAPA
360 370 380 390 400
GTFITCYLGE VITSAEAAKR DKNYDDDGIT YLFDLDMFDD ASEYTVDAQN
410 420 430 440 450
YGDVSRFFNH SCSPNIAIYS AVRNHGFRTI YDLAFFAIKD IQPLEELTFD
460 470 480 490
YAGAKDFSPV QSQKSQQNRI SKLRRQCKCG SANCRGWLFG
Length:490
Mass (Da):55,918
Last modified:December 8, 2000 - v2
Checksum:i53C3EC87BCBA51FF
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti19D → G in AAC18302 (PubMed:9620780).Curated1
Sequence conflicti142Missing AA sequence (PubMed:16024659).Curated1
Sequence conflicti437A → G in AAC18302 (PubMed:9620780).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF061854 Genomic DNA. Translation: AAC18302.1.
AJ007840 Genomic DNA. Translation: CAA07709.1.
CU329671 Genomic DNA. Translation: CAA22283.1.
PIRiT43700.
T43745.
RefSeqiNP_595186.1. NM_001021094.2.

Genome annotation databases

EnsemblFungiiSPBC428.08c.1; SPBC428.08c.1:pep; SPBC428.08c.
GeneIDi2540825.
KEGGispo:SPBC428.08c.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF061854 Genomic DNA. Translation: AAC18302.1.
AJ007840 Genomic DNA. Translation: CAA07709.1.
CU329671 Genomic DNA. Translation: CAA22283.1.
PIRiT43700.
T43745.
RefSeqiNP_595186.1. NM_001021094.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1G6ZNMR-A2-69[»]
1MVHX-ray2.30A192-490[»]
1MVXX-ray3.00A192-490[»]
ProteinModelPortaliO60016.
SMRiO60016.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi277343. 291 interactors.
DIPiDIP-32588N.
IntActiO60016. 5 interactors.
MINTiMINT-195370.

Proteomic databases

MaxQBiO60016.
PRIDEiO60016.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPBC428.08c.1; SPBC428.08c.1:pep; SPBC428.08c.
GeneIDi2540825.
KEGGispo:SPBC428.08c.

Organism-specific databases

EuPathDBiFungiDB:SPBC428.08c.
PomBaseiSPBC428.08c. clr4.

Phylogenomic databases

InParanoidiO60016.
KOiK11419.
OrthoDBiEOG092C2EWO.
PhylomeDBiO60016.

Miscellaneous databases

EvolutionaryTraceiO60016.
PROiO60016.

Family and domain databases

InterProiIPR000953. Chromo/shadow_dom.
IPR023780. Chromo_domain.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
IPR011381. Histone_H3-K9_MeTrfase.
IPR003616. Post-SET_dom.
IPR007728. Pre-SET_dom.
IPR001214. SET_dom.
[Graphical view]
PfamiPF00385. Chromo. 1 hit.
PF05033. Pre-SET. 1 hit.
PF00856. SET. 1 hit.
[Graphical view]
PIRSFiPIRSF009343. SUV39_SET. 1 hit.
SMARTiSM00298. CHROMO. 1 hit.
SM00508. PostSET. 1 hit.
SM00468. PreSET. 1 hit.
SM00317. SET. 1 hit.
[Graphical view]
SUPFAMiSSF54160. SSF54160. 1 hit.
PROSITEiPS00598. 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]
ProtoNetiSearch...

Entry informationi

Entry nameiCLR4_SCHPO
AccessioniPrimary (citable) accession number: O60016
Secondary accession number(s): O74565
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 8, 2000
Last sequence update: December 8, 2000
Last modified: November 30, 2016
This is version 161 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  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.