Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0001505
UniProt IDO60341
Primary gene name(s)KDM1A
Synonym gene name(s)AOF2, KDM1, KIAA0601, LSD1
Protein nameLysine-specific histone demethylase 1A
Protein functionHistone demethylase that demethylates both 'Lys-4', H3K4me and 'Lys-9', H3K9me of histone H3, thereby acting as a coactivator or a corepressor, depending on the context. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono-, H3K4me1 and di-methylated, H3K4me2 H3K4me. May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity. Also acts as a coactivator of androgen receptor, ANDR-dependent transcription, by being recruited to ANDR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in ANDR-containing complexes, which mediates phosphorylation of 'Thr-6' of histone H3, H3T6ph, a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A. Demethylates di-methylated 'Lys-370' of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase, HDAC recruitment, a number of genes implicated in multilineage blood cell development. Effector of SNAI1-mediated transcription repression of E-cadherin/CDH1, CDN7 and KRT8. Required for the maintenance of the silenced state of the SNAI1 target genes E-cadherin/CDH1 and CDN7. {ECO:0000269|PubMed:12032298, ECO:0000269|PubMed:15620353, ECO:0000269|PubMed:16079795, ECO:0000269|PubMed:17805299, ECO:0000269|PubMed:20228790, ECO:0000269|PubMed:20562920}.
Subcellular locationNucleus {ECO:0000269|PubMed:11102443, ECO:0000269|PubMed:16079795}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: O60341
Gene Ontology
(Biological Process)
Complete annatation
alternative mRNA splicing, via spliceosome [GO:0000380];
blood coagulation [GO:0007596];
cell proliferation [GO:0008283];
cellular response to cAMP [GO:0071320];
cellular response to gamma radiation [GO:0071480];
cellular response to UV [GO:0034644];
cerebral cortex development [GO:0021987];
granulocyte differentiation [GO:0030851];
guanine metabolic process [GO:0046098];
histone H3-K4 demethylation [GO:0034720];
histone H3-K9 demethylation [GO:0033169];
in utero embryonic development [GO:0001701];
muscle cell development [GO:0055001];
negative regulation of DNA binding [GO:0043392];
negative regulation of DNA damage response, signal transduction by p53 class mediator [GO:0043518];
negative regulation of histone H3-K4 methylation [GO:0051572];
negative regulation of histone H3-K9 methylation [GO:0051573];
negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator [GO:1902166];
negative regulation of neurogenesis [GO:0050768];
negative regulation of protein binding [GO:0032091];
negative regulation of sequence-specific DNA binding transcription factor activity [GO:0043433];
negative regulation of transcription, DNA-templated [GO:0045892];
negative regulation of transcription from RNA polymerase II promoter [GO:0000122];
neuron maturation [GO:0042551];
neuron projection extension [GO:1990138];
pituitary gland development [GO:0021983];
positive regulation of cell size [GO:0045793];
positive regulation of chromatin binding [GO:0035563];
positive regulation of erythrocyte differentiation [GO:0045648];
positive regulation of histone ubiquitination [GO:0033184];
positive regulation of hormone biosynthetic process [GO:0046886];
positive regulation of megakaryocyte differentiation [GO:0045654];
positive regulation of neural precursor cell proliferation [GO:2000179];
positive regulation of neuron projection development [GO:0010976];
positive regulation of sequence-specific DNA binding transcription factor activity [GO:0051091];
positive regulation of stem cell proliferation [GO:2000648];
positive regulation of transcription from RNA polymerase II promoter [GO:0045944];
protein demethylation [GO:0006482];
regulation of cellular protein localization [GO:1903827];
regulation of double-strand break repair via homologous recombination [GO:0010569];
regulation of primitive erythrocyte differentiation [GO:0010725];
regulation of transcription from RNA polymerase II promoter [GO:0006357];
response to fungicide [GO:0060992];
transcription, DNA-templated [GO:0006351]
Gene Ontology
(Molecular Function)
Complete annatation
androgen receptor binding [GO:0050681];
chromatin binding [GO:0003682];
demethylase activity [GO:0032451];
enzyme binding [GO:0019899];
flavin adenine dinucleotide binding [GO:0050660];
histone deacetylase activity [GO:0004407];
histone demethylase activity [GO:0032452];
histone demethylase activity, H3-dimethyl-K4 specific [GO:0034648];
histone demethylase activity, H3-K4 specific [GO:0032453];
histone demethylase activity, H3-K9 specific [GO:0032454];
ligand-dependent nuclear receptor transcription coactivator activity [GO:0030374];
MRF binding [GO:0043426];
oxidoreductase activity [GO:0016491];
p53 binding [GO:0002039];
telomeric DNA binding [GO:0042162];
telomeric repeat-containing RNA binding [GO:0061752];
transcription factor activity, sequence-specific DNA binding [GO:0003700];
transcription factor binding [GO:0008134];
transcription regulatory region DNA binding [GO:0044212]
Gene Ontology
(Cellular Component)
Complete annatation
DNA repair complex [GO:1990391];
nuclear chromatin [GO:0000790];
nuclear chromosome, telomeric region [GO:0000784];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
protein complex [GO:0043234];
transcription factor complex [GO:0005667]
Protein-protein interaction116667
Phylogenetic treeO60341
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
Brass et al., Science, 2008
Smith et al., J. Immunol, 2010
gene status
Lu et al., J. Virol., 2011
      Folds changes 8h: unknown; Folds changes 16h: unknown; Tested: unknown;
Schoggins JW and Rice CM, Curr. Opin. Virol., 2011
      Targeted viruses: unknown
      Viral life cycle: unknown
      Mechanism related to antiviral activity: unknown
Anti-viral restriction factor Liu et al., Retrovirology, 2011
      unknown (Triplicates)

Gene Expression Profile       top

            Up-regulated;            Down-regulated

For brief introduction to each study, please go to the help page.

Gene expression during HIV latency

(1). Mohammadi et al., PLoS Pathog., 2014

Differentially expressed transcripts (Pairwise) during latency and subsequent viral reactivation using several agents - Primary CD4+ T-cell based model

DMSO: Dimethyl suloxyde (negative control) - 0.0033% final
SAHA: Vorinostat (Histone deacetylase inhibitor) - 0.5 μM
CD3: TCR Stimulation by IL-2+ antiCD3/anti-CD28 antibodies
IL7: Interleukin-7 based stimulation
DISU: Disulfiram (alcohol dehydrogenase inhibitor) - 0.5 μM
AZA: 5-azacytidine (AZA; DNA methylation inhibitor) - 1 μM
Experimental Condition Log2 Fold Change P value Adjusted P value
AZA vs. CD30.6520928414476570.04730332721782550.0954169898055495
AZA vs. DISU-0.0716381884073020.777422902218620.976444104025318
AZA vs. IL70.04441675873836950.8176245115585520.999311006273513
AZA vs. SAHA0.4196613684831730.08673645861301760.368300106234543
DISU vs. CD3-0.7356745555862970.04412517601274280.0974711171184181
DISU vs. IL70.1068914635500360.6719295876500570.909766349364524
DISU vs. SAHA0.4928105997585910.09378549892942610.391318176734602
DMSO vs. AZA-0.01788264213957670.9152512152235471
DMSO vs. CD3-0.681272845009790.03389792256500220.0694131036348727
DMSO vs. DISU0.05206250855111010.8313345604694750.98111438763097
DMSO vs. IL70.0694884191617870.6997289264167570.937788846060647
DMSO vs. SAHA0.4311728110913780.06861382152426710.30516096980928
HIV vs. Mock in Activation-0.008453364794134150.9891488867385230.999983755607037
HIV vs. Mock in Latency0.009319565785951420.9550919722149380.999834320637052
IL7 vs. CD3-0.6004329803540370.06247997992436480.131384031445306
SAHA vs. CD3-0.2569679938904630.4669586490243460.578706154670797
SAHA vs. IL70.3721158108025750.1279317473753830.332834511552732
(2). Iglesias-Ussel et al., J. Virol., 2013

Up and Downregulated transcripts during Latency (Latently infected CD4+ T cells vs Uninfected)- Primary CD4+Tcell based model
Log2 Fold Change P Value
unknown unknown

Gene expression during HIV infection and replication

(1). Imbeault et al., PloS Pathog., 2012

Transcriptomic profiling of HIV-1 infected CD4+ T cells - Primary CD4+ T cells
Experiment type Log2 Fold Change P Value Adjusted P Value
Infected vs. Mock unknown unknown unknown
Infected vs. Bystander unknown unknown unknown
(2). Lefebvre et al., J. Virol., 2011

Transcriptome analysis of T-cell line (Sup T1)
Log2 Fold Change unknown
(3). Li et al., J. Immunol., 2013

Lymphatic tissue
Acute Fold Change Acute P Value Asymt Fold Change Asypt P Value AIDS Fold Change AIDS P Value
unknown unknown unknown unknown unknown unknown
(4). Chang et al., MBio., 2011

Transcriptome analysis of T-cell line (Sup T1)

Derived from Sherrill-Mix et al., BMC Retrovirol., 2015 cross validation
Up-regulated (True) FALSE
(5). Sherrill-Mix et al., BMC Retrovirol., 2015

Deep RNA-seq analysis of primary human T cell infected with low passage HIV isolate HIV89.6 - Primary CD4+ T cell based
Test Status Log2 Fold Change P Value
OK -0.0742826 0.667239
(6). Rotger et al., PLoS Pathog., 2010

Genome-wide mRNA expression of CD4+ T cells from HIV-infected patient
(Genes differentially expressed (at adjusted p<0.01) according to the empirical Bayes approach)
Log2 Fold Change P Value
unknown unknown

Proteomic/Transcriptomics studies indicating differentially expressed genes mediated by HIV

(1). Greenwood et al., Elife, 2016

Activated (CD3/CD28) Primary human CD4+ T cells infected with pNL4-3-dE-EGFP. The table shows the complete (unfiltered) TMT (tandem mass tag)-based proteomic time course dataset
6 h 24 h 48 h 72 h RTi
1.019 0.953 0.886 0.869 1.003
(2). Navare et al., Virology, 2012

SUP-T1 cell line
FC-4hpi P-value FC-8hpi P-value FC-20hpi P-value Category
unknown unknown unknown unknown unknown unknown unknown
(3). Hyrcza et al., J. Virolo., 2007

Primary human CD4+ and CD8+ T Cells
Affymetrix Prob ID Fold Change In CD8? Category
unknown unknown unknown unknown

Protein Overview       top

Drug-protein Interaction       (annotations from DrugBank)      top

not found

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
2COM NMR - A=169-279.
2DW4 X-ray 2.3Å A=172-831.
2EJR X-ray 2.7Å A=172-833.
2H94 X-ray 2.9Å A=172-835.
2HKO X-ray 2.8Å A=172-835.
2IW5 X-ray 2.5Å A=171-836.
2L3D NMR - A=174-273.
2UXN X-ray 2.7Å A=171-836.
2UXX X-ray 2.7Å A=171-836.
2V1D X-ray 3.1Å A=123-852.
2X0L X-ray 3.0Å A=123-852.
2XAF X-ray 3.2Å A=1-852.
2XAG X-ray 3.1Å A=1-852.
2XAH X-ray 3.1Å A=1-852.
2XAJ X-ray 3.3Å A=1-852.
2XAQ X-ray 3.2Å A=1-852.
2XAS X-ray 3.2Å A=1-852.
2Y48 X-ray 3.0Å A=123-852.
2Z3Y X-ray 2.2Å A=172-833.
2Z5U X-ray 2.2Å A=172-833.
3ABT X-ray 3.2Å A=172-833.
3ABU X-ray 3.1Å A=172-833.
3ZMS X-ray 2.9Å A=1-852.
3ZMT X-ray 3.1Å A=1-852.
3ZMU X-ray 3.2Å A=1-852.
3ZMV X-ray 3.0Å A=1-852.
3ZMZ X-ray 3.0Å A=1-852.
3ZN0 X-ray 2.8Å A=1-852.
3ZN1 X-ray 3.1Å A=1-852.
4BAY X-ray 3.1Å A=172-852.
4CZZ X-ray 3.0Å A=1-852.
4KUM X-ray 3.0Å A=171-836.
4UV8 X-ray 2.8Å A=1-852.
4UV9 X-ray 3.0Å A=1-852.
4UVA X-ray 2.9Å A=1-852.
4UVB X-ray 2.8Å A=1-852.
4UVC X-ray 3.1Å A=1-852.
4UXN X-ray 2.8Å A=1-852.
4XBF X-ray 2.8Å A=171-836.
5AFW X-ray 1.6Å B=108-119.
5IT3 X-ray 1.4Å A/B=183-267.
5L3B X-ray 3.3Å A=1-852.
5L3C X-ray 3.3Å A=1-852.
5L3D X-ray 2.6Å A=1-852.
5L3E X-ray 2.8Å A=123-852.
5L3F X-ray 3.5Å A=123-852.
5L3G X-ray 3.1Å A=123-852.
5LBQ X-ray 3.3Å A=123-852.

HIV-1 Interaction       (annotations from NCBI HIV-1 Interaction Database)      top

HIV Partner Interaction Type PubMed
Tat recruits 21876670
Tat modified by 21876670
Tat co-localizes with 22067449

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
not found