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Protein

Histone-lysine N-methyltransferase KMT5C

Gene

KMT5C

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Histone methyltransferase that specifically trimethylates 'Lys-20' of histone H4. H4 'Lys-20' trimethylation represents a specific tag for epigenetic transcriptional repression. Mainly functions in pericentric heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin in these regions. KMT5C is targeted to histone H3 via its interaction with RB1 family proteins (RB1, RBL1 and RBL2) (By similarity).By similarity

Catalytic activityi

S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].PROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Methyltransferase, Repressor, Transferase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciZFISH:HS13469-MONOMER.
ReactomeiR-HSA-3214841. PKMTs methylate histone lysines.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone-lysine N-methyltransferase KMT5CCurated (EC:2.1.1.43)
Alternative name(s):
Lysine N-methyltransferase 5C
Lysine-specific methyltransferase 5CImported
Suppressor of variegation 4-20 homolog 2
Short name:
Su(var)4-20 homolog 2
Short name:
Suv4-20h2
Gene namesi
Name:KMT5CImported
Synonyms:SUV420H2
ORF Names:PP7130
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

HGNCiHGNC:28405. KMT5C.

Subcellular locationi

  • Nucleus
  • Chromosome By similarity

  • Note: Associated with pericentric heterochromatin. CBX1 and CBX5 are required for the localization to pericentric heterochromatin (By similarity).By similarity

GO - Cellular componenti

  • condensed nuclear chromosome, centromeric region Source: Ensembl
  • nuclear heterochromatin Source: BHF-UCL
  • nucleoplasm Source: HPA
  • pericentric heterochromatin Source: BHF-UCL
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi84787.
OpenTargetsiENSG00000133247.
PharmGKBiPA134934307.

Chemistry databases

ChEMBLiCHEMBL2321644.
GuidetoPHARMACOLOGYi2718.

Polymorphism and mutation databases

BioMutaiSUV420H2.
DMDMi74727906.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002817931 – 462Histone-lysine N-methyltransferase KMT5CAdd BLAST462

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei416PhosphothreonineCombined sources1
Modified residuei422PhosphothreonineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ86Y97.
MaxQBiQ86Y97.
PaxDbiQ86Y97.
PeptideAtlasiQ86Y97.
PRIDEiQ86Y97.

PTM databases

iPTMnetiQ86Y97.
PhosphoSitePlusiQ86Y97.

Expressioni

Gene expression databases

BgeeiENSG00000133247.
CleanExiHS_SUV420H2.
ExpressionAtlasiQ86Y97. baseline and differential.
GenevisibleiQ86Y97. HS.

Organism-specific databases

HPAiHPA052294.

Interactioni

Subunit structurei

Interacts with HP1 proteins CBX1, CBX3 and CBX5. Interacts with RB1 family proteins RB1, RBL1 and RBL2 (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
CBX3Q131852EBI-7960569,EBI-78176

Protein-protein interaction databases

BioGridi124257. 10 interactors.
IntActiQ86Y97. 5 interactors.
MINTiMINT-4776457.
STRINGi9606.ENSP00000255613.

Chemistry databases

BindingDBiQ86Y97.

Structurei

Secondary structure

1462
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi8 – 27Combined sources20
Helixi45 – 58Combined sources14
Helixi61 – 69Combined sources9
Turni70 – 78Combined sources9
Helixi83 – 99Combined sources17
Helixi102 – 104Combined sources3
Beta strandi106 – 110Combined sources5
Beta strandi121 – 127Combined sources7
Beta strandi134 – 144Combined sources11
Helixi147 – 152Combined sources6
Turni155 – 157Combined sources3
Beta strandi162 – 165Combined sources4
Turni166 – 169Combined sources4
Beta strandi170 – 176Combined sources7
Helixi177 – 180Combined sources4
Beta strandi188 – 194Combined sources7
Turni195 – 197Combined sources3
Beta strandi198 – 205Combined sources8
Beta strandi221 – 223Combined sources3
Helixi224 – 226Combined sources3
Helixi232 – 237Combined sources6
Helixi240 – 242Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3RQ4X-ray1.80A2-248[»]
ProteinModelPortaliQ86Y97.
SMRiQ86Y97.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini104 – 218SETPROSITE-ProRule annotationAdd BLAST115

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni346 – 435Required for heterochromatin localizationBy similarityAdd BLAST90

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. Suvar4-20 subfamily.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG2589. Eukaryota.
ENOG410XPH8. LUCA.
GeneTreeiENSGT00520000055640.
HOGENOMiHOG000154453.
HOVERGENiHBG095676.
InParanoidiQ86Y97.
KOiK11429.
OMAiFCAACQP.
OrthoDBiEOG091G0IUY.
PhylomeDBiQ86Y97.
TreeFamiTF106433.

Family and domain databases

InterProiIPR025790. Hist-Lys_N-MTase_Suvar4-20.
IPR001214. SET_dom.
[Graphical view]
PfamiPF00856. SET. 1 hit.
[Graphical view]
SMARTiSM00317. SET. 1 hit.
[Graphical view]
PROSITEiPS51570. SAM_MT43_SUVAR420_2. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q86Y97-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MGPDRVTARE LCENDDLATS LVLDPYLGFR THKMNVSPVP PLRRQQHLRS
60 70 80 90 100
ALETFLRQRD LEAAYRALTL GGWTARYFQS RGPRQEAALK THVYRYLRAF
110 120 130 140 150
LPESGFTILP CTRYSMETNG AKIVSTRAWK KNEKLELLVG CIAELREADE
160 170 180 190 200
GLLRAGENDF SIMYSTRKRS AQLWLGPAAF INHDCKPNCK FVPADGNAAC
210 220 230 240 250
VKVLRDIEPG DEVTCFYGEG FFGEKNEHCE CHTCERKGEG AFRTRPREPA
260 270 280 290 300
LPPRPLDKYQ LRETKRRLQQ GLDSGSRQGL LGPRACVHPS PLRRDPFCAA
310 320 330 340 350
CQPLRLPACS ARPDTSPLWL QWLPQPQPRV RPRKRRRPRP RRAPVLSTHH
360 370 380 390 400
AARVSLHRWG GCGPHCRLRG EALVALGQPP HARWAPQQDW HWARRYGLPY
410 420 430 440 450
VVRVDLRRLA PAPPATPAPA GTPGPILIPK QALAFAPFSP PKRLRLVVSH
460
GSIDLDVGGE EL
Length:462
Mass (Da):52,113
Last modified:June 1, 2003 - v1
Checksum:i6814F7BDFA109070
GO
Isoform 2 (identifier: Q86Y97-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     37-97: SPVPPLRRQQ...ALKTHVYRYL → RSIATSVPSC...QSCGRQMRGC
     98-462: Missing.

Note: No experimental confirmation available. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
Show »
Length:97
Mass (Da):10,821
Checksum:i8E4BE260BF16E819
GO

Sequence cautioni

The sequence AAH05842 differs from that shown. Reason: Erroneous translation. Wrong choice of CDS.Curated
The sequence AAL55766 differs from that shown. Probable cloning artifact.Curated

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_04394737 – 97SPVPP…VYRYL → RSIATSVPSCRKVALPSCPA RATPWRPTGPRSCPLVLGKR MRSWSCWWAALQSCGRQMRG C in isoform 2. 1 PublicationAdd BLAST61
Alternative sequenceiVSP_04394898 – 462Missing in isoform 2. 1 PublicationAdd BLAST365

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC020922 Genomic DNA. No translation available.
BC005842 mRNA. Translation: AAH05842.1. Sequence problems.
BC019313 mRNA. Translation: AAH19313.1.
BC044889 mRNA. Translation: AAH44889.1.
AF289582 mRNA. Translation: AAL55766.1. Sequence problems.
CCDSiCCDS12922.1. [Q86Y97-1]
RefSeqiNP_116090.2. NM_032701.3. [Q86Y97-1]
XP_005259395.1. XM_005259338.3.
XP_006723505.1. XM_006723442.3.
XP_011525717.1. XM_011527415.2. [Q86Y97-1]
UniGeneiHs.590982.

Genome annotation databases

EnsembliENST00000255613; ENSP00000255613; ENSG00000133247. [Q86Y97-1]
ENST00000445196; ENSP00000397296; ENSG00000133247. [Q86Y97-2]
ENST00000592631; ENSP00000467499; ENSG00000133247. [Q86Y97-2]
GeneIDi84787.
KEGGihsa:84787.
UCSCiuc002qkj.5. human. [Q86Y97-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC020922 Genomic DNA. No translation available.
BC005842 mRNA. Translation: AAH05842.1. Sequence problems.
BC019313 mRNA. Translation: AAH19313.1.
BC044889 mRNA. Translation: AAH44889.1.
AF289582 mRNA. Translation: AAL55766.1. Sequence problems.
CCDSiCCDS12922.1. [Q86Y97-1]
RefSeqiNP_116090.2. NM_032701.3. [Q86Y97-1]
XP_005259395.1. XM_005259338.3.
XP_006723505.1. XM_006723442.3.
XP_011525717.1. XM_011527415.2. [Q86Y97-1]
UniGeneiHs.590982.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3RQ4X-ray1.80A2-248[»]
ProteinModelPortaliQ86Y97.
SMRiQ86Y97.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi124257. 10 interactors.
IntActiQ86Y97. 5 interactors.
MINTiMINT-4776457.
STRINGi9606.ENSP00000255613.

Chemistry databases

BindingDBiQ86Y97.
ChEMBLiCHEMBL2321644.
GuidetoPHARMACOLOGYi2718.

PTM databases

iPTMnetiQ86Y97.
PhosphoSitePlusiQ86Y97.

Polymorphism and mutation databases

BioMutaiSUV420H2.
DMDMi74727906.

Proteomic databases

EPDiQ86Y97.
MaxQBiQ86Y97.
PaxDbiQ86Y97.
PeptideAtlasiQ86Y97.
PRIDEiQ86Y97.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000255613; ENSP00000255613; ENSG00000133247. [Q86Y97-1]
ENST00000445196; ENSP00000397296; ENSG00000133247. [Q86Y97-2]
ENST00000592631; ENSP00000467499; ENSG00000133247. [Q86Y97-2]
GeneIDi84787.
KEGGihsa:84787.
UCSCiuc002qkj.5. human. [Q86Y97-1]

Organism-specific databases

CTDi84787.
DisGeNETi84787.
GeneCardsiSUV420H2.
H-InvDBHIX0174420.
HGNCiHGNC:28405. KMT5C.
HPAiHPA052294.
MIMi613198. gene.
neXtProtiNX_Q86Y97.
OpenTargetsiENSG00000133247.
PharmGKBiPA134934307.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2589. Eukaryota.
ENOG410XPH8. LUCA.
GeneTreeiENSGT00520000055640.
HOGENOMiHOG000154453.
HOVERGENiHBG095676.
InParanoidiQ86Y97.
KOiK11429.
OMAiFCAACQP.
OrthoDBiEOG091G0IUY.
PhylomeDBiQ86Y97.
TreeFamiTF106433.

Enzyme and pathway databases

BioCyciZFISH:HS13469-MONOMER.
ReactomeiR-HSA-3214841. PKMTs methylate histone lysines.

Miscellaneous databases

ChiTaRSiSUV420H2. human.
GenomeRNAii84787.
PROiQ86Y97.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000133247.
CleanExiHS_SUV420H2.
ExpressionAtlasiQ86Y97. baseline and differential.
GenevisibleiQ86Y97. HS.

Family and domain databases

InterProiIPR025790. Hist-Lys_N-MTase_Suvar4-20.
IPR001214. SET_dom.
[Graphical view]
PfamiPF00856. SET. 1 hit.
[Graphical view]
SMARTiSM00317. SET. 1 hit.
[Graphical view]
PROSITEiPS51570. SAM_MT43_SUVAR420_2. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiKMT5C_HUMAN
AccessioniPrimary (citable) accession number: Q86Y97
Secondary accession number(s): Q8WZ10, Q9BRZ6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: June 1, 2003
Last modified: November 30, 2016
This is version 124 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.