KDM4A

Available structures

Ortholog search: PDBe RCSB

List of PDB id codes
2GF7, 2GFA, 2GP3, 2GP5, 2OQ6, 2OQ7, 2OS2, 2OT7, 2OX0, 2P5B, 2PXJ, 2Q8C, 2Q8D, 2Q8E, 2QQR, 2QQS, 2VD7, 2WWJ, 2YBK, 2YBP, 2YBS, 3NJY, 3PDQ, 3RVH, 3U4S, 4AI9, 4BIS, 4GD4, 4URA, 4V2V, 4V2W, 5D6X, 5F5I, 5A7S, 5F2S, 5A7N, 5A7Q, 5A7O, 5F2W, 5D6W, 5F32, 5FPV, 5A7P, 5A7W, 5F3I, 5A80, 5F37, 5F3E, 5F39, 5F3G, 5F3C, 5D6Y, 5FYC, 5FYI, 5FY8, 5FWE, 5ANQ, 5FYH

Identifiers

Aliases

KDM4A, JHDM3A, JMJD2, JMJD2A, TDRD14A, lysine demethylase 4A

External IDs

MGI: 2446210 HomoloGene: 27780 GeneCards: KDM4A

Gene ontology
Molecular function	• zinc ion binding • dioxygenase activity • metal ion binding • methylated histone binding • protein binding • histone demethylase activity (H3-K36 specific) • oxidoreductase activity • ubiquitin protein ligase binding • double-stranded DNA binding • histone demethylase activity
Cellular component	• pericentric heterochromatin • nucleoplasm • nucleolus • nucleus • cytoplasm
Biological process	• histone demethylation • regulation of transcription, DNA-templated • negative regulation of gene expression • transcription, DNA-templated • cardiac muscle hypertrophy in response to stress • negative regulation of histone H3-K9 trimethylation • viral process • negative regulation of transcription, DNA-templated • negative regulation of autophagy • oxidation-reduction process • negative regulation of cell death • negative regulation of astrocyte differentiation • positive regulation of gene expression • response to nutrient levels • histone H3-K36 demethylation • positive regulation of neuron differentiation • covalent chromatin modification
Sources:Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

Entrez


9682


230674

Ensembl


ENSG00000066135


ENSMUSG00000033326

UniProt


O75164


Q8BW72

RefSeq (mRNA)


NM_014663


NM_001161823 NM_172382

RefSeq (protein)


NP_055478.2


NP_001155295.1 NP_759014.2

Location (UCSC)

Chr 1: 43.65 – 43.71 Mb

Chr 4: 118.14 – 118.18 Mb

PubMed search

^[1]

^[2]

Wikidata

View/Edit Human

View/Edit Mouse

Lysine-specific demethylase 4A is an enzyme that in humans is encoded by the KDM4A gene.^[3]^[4]^[5]

Function

This gene is a member of the Jumonji domain 2 (JMJD2) family and encodes a protein with a JmjN domain, a JmjC domain, a JD2H domain, two TUDOR domains, and two PHD-type zinc fingers. This nuclear protein functions as a trimethylation-specific demethylase, converting specific trimethylated histone on histone H3 lysine 9 and 36 residues to the dimethylated form and lysine 9 dimethylated residues to monomethyl, and as a transcriptional repressor.^[5]

Alterations in this gene have been found associated with chromosomal instability that leads to cancer.(PMID 23871696)

References

↑ "Human PubMed Reference:".
↑ "Mouse PubMed Reference:".
↑ Ishikawa K, Nagase T, Suyama M, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O (June 1998). "Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro". DNA Research. 5 (3): 169–76. doi:10.1093/dnares/5.3.169. PMID 9734811.
↑ Katoh M, Katoh M (June 2004). "Identification and characterization of JMJD2 family genes in silico". International Journal of Oncology. 24 (6): 1623–8. doi:10.3892/ijo.25.3.759. PMID 15138608.
1 2 "Entrez Gene: JMJD2A jumonji domain containing 2A".

Bonaldo MF, Lennon G, Soares MB (September 1996). "Normalization and subtraction: two approaches to facilitate gene discovery". Genome Research. 6 (9): 791–806. doi:10.1101/gr.6.9.791. PMID 8889548.
Yoon HG, Chan DW, Reynolds AB, Qin J, Wong J (September 2003). "N-CoR mediates DNA methylation-dependent repression through a methyl CpG binding protein Kaiso". Molecular Cell. 12 (3): 723–34. doi:10.1016/j.molcel.2003.08.008. PMID 14527417.
Brandenberger R, Wei H, Zhang S, Lei S, Murage J, Fisk GJ, Li Y, Xu C, Fang R, Guegler K, Rao MS, Mandalam R, Lebkowski J, Stanton LW (June 2004). "Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation". Nature Biotechnology. 22 (6): 707–16. doi:10.1038/nbt971. PMID 15146197.
Suzuki Y, Yamashita R, Shirota M, Sakakibara Y, Chiba J, Mizushima-Sugano J, Nakai K, Sugano S (September 2004). "Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions". Genome Research. 14 (9): 1711–8. doi:10.1101/gr.2435604. PMC 515316. PMID 15342556.
Gray SG, Iglesias AH, Lizcano F, Villanueva R, Camelo S, Jingu H, Teh BT, Koibuchi N, Chin WW, Kokkotou E, Dangond F (August 2005). "Functional characterization of JMJD2A, a histone deacetylase- and retinoblastoma-binding protein". The Journal of Biological Chemistry. 280 (31): 28507–18. doi:10.1074/jbc.M413687200. PMID 15927959.
Zhang D, Yoon HG, Wong J (August 2005). "JMJD2A is a novel N-CoR-interacting protein and is involved in repression of the human transcription factor achaete scute-like homologue 2 (ASCL2/Hash2)". Molecular and Cellular Biology. 25 (15): 6404–14. doi:10.1128/MCB.25.15.6404-6414.2005. PMC 1190321. PMID 16024779.
Tao WA, Wollscheid B, O'Brien R, Eng JK, Li XJ, Bodenmiller B, Watts JD, Hood L, Aebersold R (August 2005). "Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry". Nature Methods. 2 (8): 591–8. doi:10.1038/nmeth776. PMID 16094384.
Kim J, Daniel J, Espejo A, Lake A, Krishna M, Xia L, Zhang Y, Bedford MT (April 2006). "Tudor, MBT and chromo domains gauge the degree of lysine methylation". EMBO Reports. 7 (4): 397–403. doi:10.1038/sj.embor.7400625. PMC 1456902. PMID 16415788.
Huang Y, Fang J, Bedford MT, Zhang Y, Xu RM (May 2006). "Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A". Science. 312 (5774): 748–51. doi:10.1126/science.1125162. PMID 16601153.
Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z, Spooner E, Li E, Zhang G, Colaiacovo M, Shi Y (May 2006). "Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases". Cell. 125 (3): 467–81. doi:10.1016/j.cell.2006.03.028. PMID 16603238.
Chen Z, Zang J, Whetstine J, Hong X, Davrazou F, Kutateladze TG, Simpson M, Mao Q, Pan CH, Dai S, Hagman J, Hansen K, Shi Y, Zhang G (May 2006). "Structural insights into histone demethylation by JMJD2 family members". Cell. 125 (4): 691–702. doi:10.1016/j.cell.2006.04.024. PMID 16677698.
Klose RJ, Yamane K, Bae Y, Zhang D, Erdjument-Bromage H, Tempst P, Wong J, Zhang Y (July 2006). "The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36". Nature. 442 (7100): 312–6. doi:10.1038/nature04853. PMID 16732292.
Shin S, Janknecht R (August 2007). "Activation of androgen receptor by histone demethylases JMJD2A and JMJD2D". Biochemical and Biophysical Research Communications. 359 (3): 742–6. doi:10.1016/j.bbrc.2007.05.179. PMID 17555712.
Chen Z, Zang J, Kappler J, Hong X, Crawford F, Wang Q, Lan F, Jiang C, Whetstine J, Dai S, Hansen K, Shi Y, Zhang G (June 2007). "Structural basis of the recognition of a methylated histone tail by JMJD2A". Proceedings of the National Academy of Sciences of the United States of America. 104 (26): 10818–23. doi:10.1073/pnas.0704525104. PMC 1891149. PMID 17567753.
Ng SS, Kavanagh KL, McDonough MA, Butler D, Pilka ES, Lienard BM, Bray JE, Savitsky P, Gileadi O, von Delft F, Rose NR, Offer J, Scheinost JC, Borowski T, Sundstrom M, Schofield CJ, Oppermann U (July 2007). "Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity". Nature. 448 (7149): 87–91. doi:10.1038/nature05971. PMID 17589501.
Lee J, Thompson JR, Botuyan MV, Mer G (January 2008). "Distinct binding modes specify the recognition of methylated histones H3K4 and H4K20 by JMJD2A-tudor". Nature Structural & Molecular Biology. 15 (1): 109–11. doi:10.1038/nsmb1326. PMC 2211384. PMID 18084306.

PDB gallery

2gf7: Double tudor domain structure

2gfa: double tudor domain complex structure

2gp3: Crystal structure of the catalytic core comain of jmjd2a

2gp5: Crystal structure of catalytic core domain of jmjd2A complexed with alpha-Ketoglutarate

2oq6: Crystal structure of JMJD2A complexed with histone H3 peptide trimethylated at Lys9

2oq7: The crystal structure of JMJD2A complexed with Ni and N-oxalylglycine

2os2: Crystal structure of JMJD2A complexed with histone H3 peptide trimethylated at Lys36

2ot7: Crystal structure of JMJD2A complexed with histone H3 peptide monomethylated at Lys9

2ox0: Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9

Oxidoreductases: dioxygenases, including steroid hydroxylases (EC 1.14)

1.14.11: 2-oxoglutarate	Prolyl hydroxylase Lysyl hydroxylase

1.14.13: NADH or NADPH	Flavin-containing monooxygenase FMO1 FMO2 FMO3 FMO4 FMO5 Nitric oxide synthase NOS1 NOS2 NOS3 Cholesterol 7 alpha-hydroxylase Methane monooxygenase 3A4 Lanosterol 14 alpha-demethylase 24-hydroxycholesterol 7α-hydroxylase

1.14.14: reduced flavin or flavoprotein	19A1 2D6 2E1

1.14.15: reduced iron-sulfur protein	11B1 11B2 11A1

1.14.16: reduced pteridine (BH4 dependent)	Phenylalanine hydroxylase Tyrosine hydroxylase Tryptophan hydroxylase

1.14.17: reduced ascorbate	Dopamine beta-hydroxylase

1.14.18-19: other	Tyrosinase Stearoyl-CoA desaturase-1

1.14.99 - miscellaneous	Cyclooxygenase Heme oxygenase (HMOX1) Squalene monooxygenase 17A1 21A2

Enzymes

Activity	Active site Binding site Catalytic triad Oxyanion hole Enzyme promiscuity Catalytically perfect enzyme Coenzyme Cofactor Enzyme catalysis Enzyme kinetics Lineweaver–Burk plot Michaelis–Menten kinetics

Regulation	Allosteric regulation Cooperativity Enzyme inhibitor

Classification	EC number Enzyme superfamily Enzyme family List of enzymes

Types	EC1 Oxidoreductases (list) EC2 Transferases (list) EC3 Hydrolases (list) EC4 Lyases (list) EC5 Isomerases (list) EC6 Ligases (list)

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KDM4A

Function

References

Further reading