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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: -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 + N6-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

GO - Biological processi

Keywordsi

Molecular functionChromatin regulator, Methyltransferase, Transferase
LigandMetal-binding, S-adenosyl-L-methionine, Zinc

Enzyme and pathway databases

ReactomeiR-SPO-3214841 PKMTs methylate histone lysines
R-SPO-427359 SIRT1 negatively regulates rRNA expression

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

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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
PaxDbiO60016
PRIDEiO60016

PTM databases

iPTMnetiO60016

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

GO - Molecular functioni

Protein-protein interaction databases

BioGridi277343, 299 interactors
DIPiDIP-32588N
IntActiO60016, 8 interactors
MINTiO60016
STRINGi4896.SPBC428.08c.1

Structurei

Secondary structure

1490
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

Phylogenomic databases

InParanoidiO60016
KOiK11419
OMAiNCRGWLF
OrthoDBiEOG092C2EWO
PhylomeDBiO60016

Family and domain databases

CDDicd00024 CHROMO, 1 hit
InterProiView protein in InterPro
IPR016197 Chromo-like_dom_sf
IPR000953 Chromo/chromo_shadow_dom
IPR023780 Chromo_domain
IPR023779 Chromodomain_CS
IPR011381 Histone_H3-K9_MeTrfase
IPR003616 Post-SET_dom
IPR007728 Pre-SET_dom
IPR001214 SET_dom
PfamiView protein in Pfam
PF00385 Chromo, 1 hit
PF05033 Pre-SET, 1 hit
PF00856 SET, 1 hit
PIRSFiPIRSF009343 SUV39_SET, 1 hit
SMARTiView protein in SMART
SM00298 CHROMO, 1 hit
SM00508 PostSET, 1 hit
SM00468 PreSET, 1 hit
SM00317 SET, 1 hit
SUPFAMiSSF54160 SSF54160, 1 hit
PROSITEiView protein in 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

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

Similar proteinsi

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[»]
6BOXX-ray2.41A/B192-490[»]
6BP4X-ray2.77A/B192-490[»]
ProteinModelPortaliO60016
SMRiO60016
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi277343, 299 interactors
DIPiDIP-32588N
IntActiO60016, 8 interactors
MINTiO60016
STRINGi4896.SPBC428.08c.1

PTM databases

iPTMnetiO60016

Proteomic databases

MaxQBiO60016
PaxDbiO60016
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
OMAiNCRGWLF
OrthoDBiEOG092C2EWO
PhylomeDBiO60016

Enzyme and pathway databases

ReactomeiR-SPO-3214841 PKMTs methylate histone lysines
R-SPO-427359 SIRT1 negatively regulates rRNA expression

Miscellaneous databases

EvolutionaryTraceiO60016
PROiPR:O60016

Family and domain databases

CDDicd00024 CHROMO, 1 hit
InterProiView protein in InterPro
IPR016197 Chromo-like_dom_sf
IPR000953 Chromo/chromo_shadow_dom
IPR023780 Chromo_domain
IPR023779 Chromodomain_CS
IPR011381 Histone_H3-K9_MeTrfase
IPR003616 Post-SET_dom
IPR007728 Pre-SET_dom
IPR001214 SET_dom
PfamiView protein in Pfam
PF00385 Chromo, 1 hit
PF05033 Pre-SET, 1 hit
PF00856 SET, 1 hit
PIRSFiPIRSF009343 SUV39_SET, 1 hit
SMARTiView protein in SMART
SM00298 CHROMO, 1 hit
SM00508 PostSET, 1 hit
SM00468 PreSET, 1 hit
SM00317 SET, 1 hit
SUPFAMiSSF54160 SSF54160, 1 hit
PROSITEiView protein in 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
ProtoNetiSearch...

Entry informationi

Entry nameiCLR4_SCHPO
AccessioniPrimary (citable) accession number: O60016
Secondary accession number(s): O74565
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 8, 2000
Last sequence update: December 8, 2000
Last modified: November 7, 2018
This is version 177 of the entry and version 2 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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