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Protein

Histone-lysine N-methyltransferase KMT5B

Gene

KMT5B

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. KMT5B is targeted to histone H3 via its interaction with RB1 family proteins (RB1, RBL1 and RBL2) (By similarity). Plays a role in myogenesis by regulating the expression of target genes, such as EID3.By similarity1 Publication

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

Myogenesis, Transcription, Transcription regulation

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciZFISH:HS12712-MONOMER.
ReactomeiR-HSA-3214841. PKMTs methylate histone lysines.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone-lysine N-methyltransferase KMT5BCurated (EC:2.1.1.43)
Alternative name(s):
Lysine N-methyltransferase 5B
Lysine-specific methyltransferase 5BImported
Suppressor of variegation 4-20 homolog 1
Short name:
Su(var)4-20 homolog 1
Short name:
Suv4-20h1
Gene namesi
Name:KMT5BImported
Synonyms:SUV420H1
ORF Names:CGI-85
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

HGNCiHGNC:24283. KMT5B.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi51111.
PharmGKBiPA134958369.

Chemistry databases

ChEMBLiCHEMBL2321645.
GuidetoPHARMACOLOGYi2717.

Polymorphism and mutation databases

BioMutaiSUV420H1.
DMDMi332278247.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002817871 – 885Histone-lysine N-methyltransferase KMT5BAdd BLAST885

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki555Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

EPDiQ4FZB7.
MaxQBiQ4FZB7.
PaxDbiQ4FZB7.
PeptideAtlasiQ4FZB7.
PRIDEiQ4FZB7.

PTM databases

iPTMnetiQ4FZB7.
PhosphoSitePlusiQ4FZB7.

Expressioni

Inductioni

Strongly down-regulated in breast cancer cells.1 Publication

Gene expression databases

BgeeiENSG00000110066.
ExpressionAtlasiQ4FZB7. baseline and differential.
GenevisibleiQ4FZB7. HS.

Organism-specific databases

HPAiHPA046139.
HPA063648.

Interactioni

Subunit structurei

Interacts with HP1 proteins CBX1, CBX3 and CBX5. Interacts with RB1 family proteins RB1, RBL1 and RBL2 (By similarity). Interacts (via C-terminus) with FRG1.By similarity1 Publication

Protein-protein interaction databases

BioGridi119300. 5 interactors.
DIPiDIP-48656N.
IntActiQ4FZB7. 5 interactors.
STRINGi9606.ENSP00000305899.

Chemistry databases

BindingDBiQ4FZB7.

Structurei

Secondary structure

1885
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi74 – 93Combined sources20
Helixi134 – 147Combined sources14
Helixi150 – 157Combined sources8
Helixi161 – 167Combined sources7
Helixi172 – 187Combined sources16
Helixi191 – 193Combined sources3
Beta strandi195 – 200Combined sources6
Beta strandi207 – 216Combined sources10
Beta strandi223 – 234Combined sources12
Helixi236 – 242Combined sources7
Turni245 – 247Combined sources3
Beta strandi252 – 255Combined sources4
Turni256 – 259Combined sources4
Beta strandi260 – 266Combined sources7
Helixi267 – 270Combined sources4
Beta strandi278 – 285Combined sources8
Beta strandi288 – 295Combined sources8
Turni309 – 312Combined sources4
Helixi314 – 316Combined sources3
Helixi322 – 327Combined sources6
Helixi330 – 332Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3S8PX-ray1.85A/B63-335[»]
ProteinModelPortaliQ4FZB7.
SMRiQ4FZB7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini193 – 308SETPROSITE-ProRule annotationAdd BLAST116

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.
HOVERGENiHBG105761.
InParanoidiQ4FZB7.
KOiK11429.
OrthoDBiEOG091G0IUY.
PhylomeDBiQ4FZB7.
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 (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q4FZB7-1) [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
MKWLGESKIM VVNGRRNGGK LSNDHQQNQS KLQHTGKDTL KAGKNAVERR
60 70 80 90 100
SNRCNGNSGF EGQSRYVPSS GMSAKELCEN DDLATSLVLD PYLGFQTHKM
110 120 130 140 150
NTSAFPSRSS RHFSKSDSFS HNNPVRFRPI KGRQEELKEV IERFKKDEHL
160 170 180 190 200
EKAFKCLTSG EWARHYFLNK NKMQEKLFKE HVFIYLRMFA TDSGFEILPC
210 220 230 240 250
NRYSSEQNGA KIVATKEWKR NDKIELLVGC IAELSEIEEN MLLRHGENDF
260 270 280 290 300
SVMYSTRKNC AQLWLGPAAF INHDCRPNCK FVSTGRDTAC VKALRDIEPG
310 320 330 340 350
EEISCYYGDG FFGENNEFCE CYTCERRGTG AFKSRVGLPA PAPVINSKYG
360 370 380 390 400
LRETDKRLNR LKKLGDSSKN SDSQSVSSNT DADTTQEKNN ATSNRKSSVG
410 420 430 440 450
VKKNSKSRTL TRQSMSRIPA SSNSTSSKLT HINNSRVPKK LKKPAKPLLS
460 470 480 490 500
KIKLRNHCKR LEQKNASRKL EMGNLVLKEP KVVLYKNLPI KKDKEPEGPA
510 520 530 540 550
QAAVASGCLT RHAAREHRQN PVRGAHSQGE SSPCTYITRR SVRTRTNLKE
560 570 580 590 600
ASDIKLEPNT LNGYKSSVTE PCPDSGEQLQ PAPVLQEEEL AHETAQKGEA
610 620 630 640 650
KCHKSDTGMS KKKSRQGKLV KQFAKIEEST PVHDSPGKDD AVPDLMGPHS
660 670 680 690 700
DQGEHSGTVG VPVSYTDCAP SPVGCSVVTS DSFKTKDSFR TAKSKKKRRI
710 720 730 740 750
TRYDAQLILE NNSGIPKLTL RRRHDSSSKT NDQENDGMNS SKISIKLSKD
760 770 780 790 800
HDNDNNLYVA KLNNGFNSGS GSSSTKLKIQ LKRDEENRGS YTEGLHENGV
810 820 830 840 850
CCSDPLSLLE SRMEVDDYSQ YEEESTDDSS SSEGDEEEDD YDDDFEDDFI
860 870 880
PLPPAKRLRL IVGKDSIDID ISSRRREDQS LRLNA
Length:885
Mass (Da):99,187
Last modified:May 3, 2011 - v4
Checksum:iB4D4812C1F1A64AB
GO
Isoform 2 (identifier: Q4FZB7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     392-393: TS → SK
     394-885: Missing.

Show »
Length:393
Mass (Da):44,617
Checksum:iDED229EA65E36B95
GO
Isoform 3 (identifier: Q4FZB7-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     274-274: D → DLINS
     275-885: Missing.

Note: No experimental confirmation available.
Show »
Length:278
Mass (Da):31,959
Checksum:i12C45DFB622AA8AC
GO

Sequence cautioni

The sequence AAD34080 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAG36937 differs from that shown. Reason: Frameshift at positions 233, 249, 254 and 272.Curated
The sequence AAH98121 differs from that shown. Reason: Erroneous translation. Wrong choice of frame.Curated
The sequence AAI04484 differs from that shown. Reason: Frameshift at position 396.Curated
The sequence BAA90905 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti74A → P in AAD34080 (PubMed:10810093).Curated1
Sequence conflicti79E → G in AAD34080 (PubMed:10810093).Curated1
Sequence conflicti99K → Q in AAD34080 (PubMed:10810093).Curated1
Sequence conflicti108R → W in AAG36937 (PubMed:11401438).Curated1
Sequence conflicti123N → K in AAD34080 (PubMed:10810093).Curated1
Sequence conflicti135E → G in AAD34080 (PubMed:10810093).Curated1
Sequence conflicti469K → E in BAA90905 (PubMed:14702039).Curated1
Sequence conflicti483V → A in BAA90905 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0477659I → N.1 PublicationCorresponds to variant rs2512606dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_040034274D → DLINS in isoform 3. 1 Publication1
Alternative sequenceiVSP_040035275 – 885Missing in isoform 3. 1 PublicationAdd BLAST611
Alternative sequenceiVSP_024051392 – 393TS → SK in isoform 2. 2 Publications2
Alternative sequenceiVSP_024052394 – 885Missing in isoform 2. 2 PublicationsAdd BLAST492

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP002992 Genomic DNA. No translation available.
BC002522 mRNA. Translation: AAH02522.2.
BC012933 mRNA. Translation: AAH12933.2.
BC065287 mRNA. Translation: AAH65287.1.
BC087834 mRNA. Translation: AAH87834.1.
BC098121 mRNA. Translation: AAH98121.1. Sequence problems.
BC099714 mRNA. Translation: AAH99714.1.
BC103498 mRNA. Translation: AAI03499.1.
BC104483 mRNA. Translation: AAI04484.1. Frameshift.
AF264782 mRNA. Translation: AAG36937.1. Frameshift.
AF151843 mRNA. Translation: AAD34080.1. Different initiation.
AK000046 mRNA. Translation: BAA90905.1. Different initiation.
AL512763 mRNA. Translation: CAC21680.1.
CCDSiCCDS31623.1. [Q4FZB7-1]
CCDS44660.1. [Q4FZB7-2]
RefSeqiNP_001287838.1. NM_001300909.1.
NP_057112.3. NM_016028.4.
NP_060105.3. NM_017635.4.
XP_005274092.2. XM_005274035.3.
XP_011543393.1. XM_011545091.1.
XP_011543395.1. XM_011545093.2.
XP_011543396.1. XM_011545094.2.
UniGeneiHs.632120.

Genome annotation databases

EnsembliENST00000304363; ENSP00000305899; ENSG00000110066.
ENST00000401547; ENSP00000385965; ENSG00000110066.
ENST00000405515; ENSP00000385640; ENSG00000110066.
ENST00000615954; ENSP00000484858; ENSG00000110066.
GeneIDi51111.
KEGGihsa:51111.
UCSCiuc001onm.2. human. [Q4FZB7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP002992 Genomic DNA. No translation available.
BC002522 mRNA. Translation: AAH02522.2.
BC012933 mRNA. Translation: AAH12933.2.
BC065287 mRNA. Translation: AAH65287.1.
BC087834 mRNA. Translation: AAH87834.1.
BC098121 mRNA. Translation: AAH98121.1. Sequence problems.
BC099714 mRNA. Translation: AAH99714.1.
BC103498 mRNA. Translation: AAI03499.1.
BC104483 mRNA. Translation: AAI04484.1. Frameshift.
AF264782 mRNA. Translation: AAG36937.1. Frameshift.
AF151843 mRNA. Translation: AAD34080.1. Different initiation.
AK000046 mRNA. Translation: BAA90905.1. Different initiation.
AL512763 mRNA. Translation: CAC21680.1.
CCDSiCCDS31623.1. [Q4FZB7-1]
CCDS44660.1. [Q4FZB7-2]
RefSeqiNP_001287838.1. NM_001300909.1.
NP_057112.3. NM_016028.4.
NP_060105.3. NM_017635.4.
XP_005274092.2. XM_005274035.3.
XP_011543393.1. XM_011545091.1.
XP_011543395.1. XM_011545093.2.
XP_011543396.1. XM_011545094.2.
UniGeneiHs.632120.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3S8PX-ray1.85A/B63-335[»]
ProteinModelPortaliQ4FZB7.
SMRiQ4FZB7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119300. 5 interactors.
DIPiDIP-48656N.
IntActiQ4FZB7. 5 interactors.
STRINGi9606.ENSP00000305899.

Chemistry databases

BindingDBiQ4FZB7.
ChEMBLiCHEMBL2321645.
GuidetoPHARMACOLOGYi2717.

PTM databases

iPTMnetiQ4FZB7.
PhosphoSitePlusiQ4FZB7.

Polymorphism and mutation databases

BioMutaiSUV420H1.
DMDMi332278247.

Proteomic databases

EPDiQ4FZB7.
MaxQBiQ4FZB7.
PaxDbiQ4FZB7.
PeptideAtlasiQ4FZB7.
PRIDEiQ4FZB7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000304363; ENSP00000305899; ENSG00000110066.
ENST00000401547; ENSP00000385965; ENSG00000110066.
ENST00000405515; ENSP00000385640; ENSG00000110066.
ENST00000615954; ENSP00000484858; ENSG00000110066.
GeneIDi51111.
KEGGihsa:51111.
UCSCiuc001onm.2. human. [Q4FZB7-1]

Organism-specific databases

CTDi51111.
DisGeNETi51111.
GeneCardsiSUV420H1.
HGNCiHGNC:24283. KMT5B.
HPAiHPA046139.
HPA063648.
MIMi610881. gene.
neXtProtiNX_Q4FZB7.
PharmGKBiPA134958369.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2589. Eukaryota.
ENOG410XPH8. LUCA.
HOVERGENiHBG105761.
InParanoidiQ4FZB7.
KOiK11429.
OrthoDBiEOG091G0IUY.
PhylomeDBiQ4FZB7.
TreeFamiTF106433.

Enzyme and pathway databases

BioCyciZFISH:HS12712-MONOMER.
ReactomeiR-HSA-3214841. PKMTs methylate histone lysines.

Miscellaneous databases

ChiTaRSiSUV420H1. human.
GeneWikiiSUV420H1.
GenomeRNAii51111.
PROiQ4FZB7.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000110066.
ExpressionAtlasiQ4FZB7. baseline and differential.
GenevisibleiQ4FZB7. 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 nameiKMT5B_HUMAN
AccessioniPrimary (citable) accession number: Q4FZB7
Secondary accession number(s): B7WNX7
, Q3SX56, Q4V775, Q6P150, Q96E44, Q9BUL0, Q9H022, Q9H2K3, Q9NXV3, Q9Y393
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: May 3, 2011
Last modified: November 30, 2016
This is version 111 of the entry and version 4 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 11
    Human chromosome 11: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.