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Protein

Lysine-specific histone demethylase 1

Gene

lsd1

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

Catalytic component of the SWM histone demethylase complex that specifically demethylates H3K9me2, a specific tag for epigenetic transcriptional activation, thereby acting as a corepressor. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Has a role in regulating heterochromatin propagation and euchromatic transcription. Also has a gene activating role.3 Publications

Cofactori

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei301FADBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi260 – 302FADSequence analysisAdd BLAST43
Nucleotide bindingi328 – 329FADBy similarity2
DNA bindingi841 – 921HMG boxPROSITE-ProRule annotationAdd BLAST81
Nucleotide bindingi908 – 909FADBy similarity2

GO - Molecular functioni

GO - Biological processi

  • antisense RNA transcription Source: PomBase
  • chromatin remodeling Source: PomBase
  • genetic imprinting at mating-type locus Source: PomBase
  • histone H3-K9 demethylation Source: PomBase
  • regulation of meiotic cell cycle Source: PomBase
  • regulation of replication fork arrest at rDNA repeats Source: PomBase
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • replication fork arrest at mating type locus Source: PomBase

Keywordsi

Molecular functionChromatin regulator, DNA-binding, Oxidoreductase, Repressor
Biological processTranscription, Transcription regulation
LigandFAD, Flavoprotein

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific histone demethylase 1 (EC:1.-.-.-)
Gene namesi
Name:lsd1
Synonyms:saf110, swm1
ORF Names:SPBC146.09c
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:SPBC146.09c.
PomBaseiSPBC146.09c. lsd1.

Subcellular locationi

GO - Cellular componenti

  • Lsd1/2 complex Source: PomBase
  • nuclear chromatin Source: PomBase
  • nucleus Source: PomBase

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003630011 – 1000Lysine-specific histone demethylase 1Add BLAST1000

Proteomic databases

MaxQBiQ9Y802.
PRIDEiQ9Y802.

Interactioni

Subunit structurei

Component of the SWM histone demethylase complex composed of at least lsd1, lsd2, phf1 and phf2. Interacts directly with lsd2.3 Publications

Protein-protein interaction databases

BioGridi276355. 10 interactors.
MINTiMINT-4720597.
STRINGi4896.SPBC146.09c.1.

Structurei

3D structure databases

ProteinModelPortaliQ9Y802.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini153 – 249SWIRMPROSITE-ProRule annotationAdd BLAST97

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni279 – 950Demethylase activityBy similarityAdd BLAST672

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili107 – 137Sequence analysisAdd BLAST31
Coiled coili434 – 529Sequence analysisAdd BLAST96

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi9 – 44Ala-richAdd BLAST36

Sequence similaritiesi

Belongs to the flavin monoamine oxidase family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

InParanoidiQ9Y802.
OMAiTTVRNGY.
OrthoDBiEOG092C0OC4.
PhylomeDBiQ9Y802.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
1.10.30.10. 1 hit.
3.50.50.60. 1 hit.
InterProiView protein in InterPro
IPR002937. Amino_oxidase.
IPR023753. FAD/NAD-binding_dom.
IPR009071. HMG_box_dom.
IPR009057. Homeobox-like.
IPR007526. SWIRM.
IPR011991. WHTH_DNA-bd_dom.
PfamiView protein in Pfam
PF01593. Amino_oxidase. 1 hit.
PF04433. SWIRM. 1 hit.
SUPFAMiSSF46689. SSF46689. 1 hit.
SSF47095. SSF47095. 1 hit.
SSF51905. SSF51905. 2 hits.
PROSITEiView protein in PROSITE
PS50118. HMG_BOX_2. 1 hit.
PS50934. SWIRM. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9Y802-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMDLSSKDAL SDVLKDTHAQ SSDPSLWAIF GHQSSDNVHE GGNESVSVEQ
60 70 80 90 100
EIFDLSQLSE RPVSETVSKA SIPTNINGLS QVKPSALEKS QEVLSLQKLP
110 120 130 140 150
IKGRRPAGRR GRPALNTSNS LERNGTRYVS AEAPISVKSS IPAIPRVTFE
160 170 180 190 200
RLCYESAIAS NLPPNALSPL EAEMLSEILE NPTWLSLYLS IRNGICYLWH
210 220 230 240 250
RNPTLYVSFN EALGIVREKK AFPLASLAFE FLSRNGHINY GCIYIISSLK
260 270 280 290 300
LDESLSQKTV AIIGAGMAGI SCARQLTNLF AQYEQDFLSR GEKPPRIVIY
310 320 330 340 350
EASERLGGHI YTHMVPLSDN EVSEKSSLAT TVNATNECMV NLLTDSLIGM
360 370 380 390 400
PTLDSDPLYI ISSQQLSLDA VHTRNREFIL HDIENGRIDT EHVQRIFRLF
410 420 430 440 450
DALLFYFNAS ASKQPLHSLI TPPEQEFIQK LDQIGWYISI EAFPLQIKDT
460 470 480 490 500
LSEFLGNSAN TLTSLLHLTV LDLKIFEWFK EYLSQSLSVS LENVYPGSIP
510 520 530 540 550
NLNLLLGENV ASYSFKHGMA DMLNSLASTP SPLPILFDQC VHTVKLEDNT
560 570 580 590 600
VNLSFVNETT VSVDKVVICI PMDKLNTHLI TFEPPLEEKK LKAIDRCHFT
610 620 630 640 650
NVKKVILIFK TQFWEPNISI FGSLPQDSGR NFIFNDCTRF YEHPTLSVFV
660 670 680 690 700
KVEGIDFMKD DDIVNGIVSQ LKKVYKPKSE AINPIRTIIS NWENNSYTNH
710 720 730 740 750
SSYQISNLFL EEDYAILSEP IDNTVFFASE AISQKNSGSI RGAFDSGILA
760 770 780 790 800
ARDVLASLIG NVVLPNTLVI EENLEQPRKT YGTKRNAQQA LGKEGERENK
810 820 830 840 850
EKRISYHTEY LRLRQKRLDK EQQECDLLIA ELLGPSPVPP SRPSANPYLL
860 870 880 890 900
YQKTQWHVCK TLADQDKQRV TGDPEARATK NEIRAKLGKT WRALDSLGKQ
910 920 930 940 950
PWVDEINARR ANYSTRLEEY QRQINSYNVR VAQIKSEHQR RCESQPIPED
960 970 980 990 1000
EAKLKLLAEQ EDEHLHPEKE GMSVENSDDD YHDDLDYEDS ISEVFPDNFS
Length:1,000
Mass (Da):112,829
Last modified:November 1, 1999 - v1
Checksum:i4E97DD0145FD4211
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329671 Genomic DNA. Translation: CAB46762.1.
AB027980 Genomic DNA. Translation: BAA87284.1.
PIRiT39423.
RefSeqiNP_595398.1. NM_001021305.2.

Genome annotation databases

EnsemblFungiiSPBC146.09c.1; SPBC146.09c.1:pep; SPBC146.09c.
GeneIDi2539805.
KEGGispo:SPBC146.09c.

Similar proteinsi

Entry informationi

Entry nameiLSD1_SCHPO
AccessioniPrimary (citable) accession number: Q9Y802
Secondary accession number(s): Q9UTV0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 10, 2009
Last sequence update: November 1, 1999
Last modified: July 5, 2017
This is version 110 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families