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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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi260 – 2601Zinc 1
Metal bindingi260 – 2601Zinc 2
Metal bindingi262 – 2621Zinc 1
Metal bindingi268 – 2681Zinc 1
Metal bindingi268 – 2681Zinc 3
Metal bindingi276 – 2761Zinc 1
Metal bindingi278 – 2781Zinc 2
Metal bindingi307 – 3071Zinc 2
Metal bindingi307 – 3071Zinc 3
Metal bindingi311 – 3111Zinc 2
Metal bindingi313 – 3131Zinc 3
Metal bindingi317 – 3171Zinc 3
Binding sitei381 – 3811S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei406 – 4061S-adenosyl-L-methioninePROSITE-ProRule annotation
Metal bindingi412 – 4121Zinc 4By similarity
Metal bindingi477 – 4771Zinc 4By similarity
Metal bindingi479 – 4791Zinc 4By similarity
Metal bindingi484 – 4841Zinc 4By similarity

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

Enzyme and pathway databases

ReactomeiR-SPO-3214841. PKMTs methylate histone lysines.

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
  • mating-type region heterochromatin Source: PomBase
  • mitotic spindle pole body Source: PomBase
  • nuclear pericentric heterochromatin Source: PomBase
  • nuclear subtelomeric heterochromatin Source: PomBase
  • nucleus Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Cytoplasm, Cytoskeleton, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi31 – 311W → G: Weak effect on methyltransferase activity. 1 Publication
Mutagenesisi41 – 411W → G: Weak effect on methyltransferase activity. 1 Publication
Mutagenesisi320 – 3201R → H: Abolishes methyltransferase activity. 1 Publication
Mutagenesisi378 – 3781G → S: Abolishes methyltransferase activity. 1 Publication
Mutagenesisi486 – 4861G → D: Abolishes methyltransferase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 490490Histone-lysine N-methyltransferase, H3 lysine-9 specificPRO_0000186063Add
BLAST

Proteomic databases

MaxQBiO60016.

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 interactions.
DIPiDIP-32588N.
IntActiO60016. 5 interactions.
MINTiMINT-195370.

Structurei

Secondary structure

1
490
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi14 – 174Combined sources
Beta strandi26 – 294Combined sources
Turni32 – 354Combined sources
Beta strandi40 – 423Combined sources
Helixi44 – 474Combined sources
Helixi51 – 6111Combined sources
Turni62 – 654Combined sources
Helixi196 – 21419Combined sources
Beta strandi216 – 2194Combined sources
Beta strandi221 – 2244Combined sources
Beta strandi226 – 2283Combined sources
Beta strandi237 – 2393Combined sources
Helixi254 – 2563Combined sources
Beta strandi265 – 2684Combined sources
Turni273 – 2753Combined sources
Beta strandi277 – 2793Combined sources
Beta strandi294 – 2963Combined sources
Beta strandi302 – 3054Combined sources
Beta strandi311 – 3133Combined sources
Helixi322 – 3243Combined sources
Beta strandi330 – 3345Combined sources
Beta strandi336 – 34611Combined sources
Beta strandi353 – 3564Combined sources
Beta strandi360 – 3634Combined sources
Helixi364 – 3718Combined sources
Beta strandi382 – 3854Combined sources
Beta strandi390 – 3923Combined sources
Beta strandi394 – 3974Combined sources
Beta strandi399 – 4024Combined sources
Helixi404 – 4074Combined sources
Beta strandi415 – 4239Combined sources
Beta strandi432 – 4398Combined sources
Beta strandi455 – 4584Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1G6ZNMR-A2-69[»]
1MVHX-ray2.30A192-490[»]
1MVXX-ray3.00A192-490[»]
ProteinModelPortaliO60016.
SMRiO60016. Positions 2-69, 193-461.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO60016.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini8 – 6962ChromoPROSITE-ProRule annotationAdd
BLAST
Domaini258 – 32568Pre-SETPROSITE-ProRule annotationAdd
BLAST
Domaini328 – 452125SETPROSITE-ProRule annotationAdd
BLAST
Domaini473 – 48917Post-SETPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni338 – 3403S-adenosyl-L-methionine bindingBy similarity
Regioni409 – 4102S-adenosyl-L-methionine bindingBy similarity

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti19 – 191D → G in AAC18302 (PubMed:9620780).Curated
Sequence conflicti142 – 1421Missing AA sequence (PubMed:16024659).Curated
Sequence conflicti437 – 4371A → G in AAC18302 (PubMed:9620780).Curated

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
EntryMethodResolution (Å)ChainPositionsPDBsum
1G6ZNMR-A2-69[»]
1MVHX-ray2.30A192-490[»]
1MVXX-ray3.00A192-490[»]
ProteinModelPortaliO60016.
SMRiO60016. Positions 2-69, 193-461.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Proteomic databases

MaxQBiO60016.

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.

Enzyme and pathway databases

ReactomeiR-SPO-3214841. PKMTs methylate histone lysines.

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: September 7, 2016
This is version 158 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.