KDM4B

KDM4B
Available structures
PDB	Ortholog search: PDBe RCSB
List of PDB id codes
	4LXL, 4UC4
Identifiers
Aliases	KDM4B , JMJD2B, TDRD14B, lysine demethylase 4B, MRD65
External IDs	OMIM: 609765 MGI: 2442355 HomoloGene: 27773 GeneCards: KDM4B
Gene location (Human)
Chr.	Chromosome 19 (human)
End	5,153,598 bp
Gene location (Mouse)
Chr.	Chromosome 17 (mouse)
End	56,709,870 bp
RNA expression pattern
	Top expressed in
	corpus epididymis; ; blood; ; caput epididymis; ; inferior olivary nucleus; ; sural nerve; ; parotid gland; ; nipple; ; lactiferous duct; ; right lobe of thyroid gland; ; left lobe of thyroid gland;
	Top expressed in
	lip; ; superior frontal gyrus; ; external carotid artery; ; neural tube; ; cerebellar cortex; ; internal carotid artery; ; mirror; ; ganglionic eminence; ; saccule; ; olfactory tubercle;
	More reference expression data
	; ; ; ;
	More reference expression data
Gene ontology
Molecular function	oxidoreductase activity ; dioxygenase activity ; metal ion binding ; histone demethylase activity ; histone H3-methyl-lysine-36 demethylase activity ; histone H3-methyl-lysine-9 demethylase activity ; DNA-binding transcription repressor activity, RNA polymerase II-specific ; chromatin binding ; methylated histone binding ;
Cellular component	nucleoplasm ; nucleus ; histone methyltransferase complex ;
Biological process	regulation of transcription, DNA-templated ; transcription, DNA-templated ; histone H3-K36 demethylation ; histone H3-K9 demethylation ; chromatin organization ; negative regulation of transcription by RNA polymerase II ; chromatin remodeling ;
	Sources:Amigo / QuickGO
Orthologs
	23030
	193796
	ENSG00000127663
	ENSMUSG00000024201
	O94953
	Q91VY5
	NM_015015 ; NM_001370093 ; NM_001370094
	NM_172132 ; NM_001357909
	NP_055830 ; NP_001357022 ; NP_001357023
	NP_742144 ; NP_001344838
	Wikidata
View/Edit Human	View/Edit Mouse

Last updated September 30, 2022

Lysine-specific demethylase 4B is an enzyme that in humans is encoded by the KDM4B gene.^[5]^[6]^[7] KDM4B belongs to the alpha-ketoglutarate-dependent hydroxylase superfamily.

Related Research Articles

Demethylases are enzymes that remove methyl (CH₃) groups from nucleic acids, proteins (particularly histones), and other molecules. Demethylases are important epigenetic proteins, as they are responsible for transcriptional regulation of the genome by controlling the methylation of DNA and histones, and by extension, the chromatin state at specific gene loci.

REST corepressor 1 also known as CoREST is a protein that in humans is encoded by the RCOR1 gene.

Lysine-specific demethylase 5D is an enzyme that in humans is encoded by the KDM5D gene. KDM5D belongs to the alpha-ketoglutarate-dependent hydroxylases superfamily.

Lysine-specific demethylase 4A is an enzyme that in humans is encoded by the KDM4A gene.

Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 is an enzyme that in humans is encoded by the JMJD6 gene.

PAS domain-containing serine/threonine-protein kinase is an enzyme that in humans is encoded by the PASK gene.

KIAA1967, also known as Deleted in Breast Cancer 1, is a protein which in humans is encoded by the KIAA1967 gene.

Rho GTPase-activating protein 4 is an enzyme that in humans is encoded by the ARHGAP4 gene. It has been shown to regulate cell motility and axonal outgrowth in vitro.

Lysine-specific demethylase 2A (KDM2A) also known as F-box and leucine-rich repeat protein 11 (FBXL11) is an enzyme that in humans is encoded by the KDM2A gene. KDM2A is a member of the superfamily of alpha-ketoglutarate-dependent hydroxylases, which are non-haem iron-containing proteins.

PHD finger protein 3 is a protein that in humans is encoded by the PHF3 gene.

Lysine-specific demethylase 3B is an enzyme that in humans is encoded by the KDM3B gene. KDM3B belongs to the alpha-ketoglutarate-dependent hydroxylase superfamily.

Zinc fingers and homeoboxes protein 3 is a protein that in humans is encoded by the ZHX3 gene.

SLIT-ROBO Rho GTPase-activating protein 3 is an enzyme that in humans is encoded by the SRGAP3 gene.

Condensin complex subunit 1 also known as chromosome-associated protein D2 (CAP-D2) or non-SMC condensin I complex subunit D2 (NCAPD2) or XCAP-D2 homolog is a protein that in humans is encoded by the NCAPD2 gene. CAP-D2 is a subunit of condensin I, a large protein complex involved in chromosome condensation.

Lysine-specific demethylase 6A also known as Ubiquitously transcribed tetratricopeptide repeat, X chromosome (UTX), is a protein which in humans is encoded by the KDM6A gene. It belongs to the 2-oxoglutarate (2OG)-dependent dioxygenase superfamily.

Lysine-specific demethylase 4C is an enzyme that in humans is encoded by the KDM4C gene.

Extended synaptotagmin-2 is a protein that in humans is encoded by the ESYT2 gene.

CDK12 cyclin-dependent kinase 12 is a protein kinase that in humans is encoded by the CDK12 gene. This enzyme is a member of cyclin-dependent kinase protein family.

Lysine-specific demethylase 4D is an enzyme that in humans is encoded by the KDM4D gene. KDM4D belongs to the alpha-ketoglutarate-dependent hydroxylase superfamily.

Zinc finger and BTB domain-containing protein 40 is a protein that in humans is encoded by the ZBTB40 gene.

References

1 2 3 GRCh38: Ensembl release 89: ENSG00000127663 - Ensembl, May 2017
1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000024201 - Ensembl, May 2017
↑ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
↑ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
↑ Nagase T, Ishikawa K, Suyama M, Kikuno R, Hirosawa M, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O (May 1999). "Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Res. 5 (6): 355–64. doi: 10.1093/dnares/5.6.355 . PMID 10048485.
↑ Katoh M, Katoh M (May 2004). "Identification and characterization of JMJD2 family genes in silico". Int J Oncol. 24 (6): 1623–8. doi:10.3892/ijo.25.3.759. PMID 15138608.
↑ "Entrez Gene: JMJD2B jumonji domain containing 2B".

Nakajima D, Okazaki N, Yamakawa H, et al. (2003). "Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones". DNA Res. 9 (3): 99–106. doi: 10.1093/dnares/9.3.99 . PMID 12168954.
Andersson B, Wentland MA, Ricafrente JY, et al. (1996). "A "double adaptor" method for improved shotgun library construction". Anal. Biochem. 236 (1): 107–13. doi:10.1006/abio.1996.0138. PMID 8619474.
Yu W, Andersson B, Worley KC, et al. (1997). "Large-scale concatenation cDNA sequencing". Genome Res. 7 (4): 353–8. doi:10.1101/gr.7.4.353. PMC 139146 . PMID 9110174.
Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. Bibcode:2002PNAS...9916899M. doi: 10.1073/pnas.242603899 . PMC 139241 . PMID 12477932.
Grimwood J, Gordon LA, Olsen A, et al. (2004). "The DNA sequence and biology of human chromosome 19". Nature. 428 (6982): 529–35. Bibcode:2004Natur.428..529G. doi: 10.1038/nature02399 . PMID 15057824.
Beausoleil SA, Jedrychowski M, Schwartz D, et al. (2004). "Large-scale characterization of HeLa cell nuclear phosphoproteins". Proc. Natl. Acad. Sci. U.S.A. 101 (33): 12130–5. Bibcode:2004PNAS..10112130B. doi: 10.1073/pnas.0404720101 . PMC 514446 . PMID 15302935.
Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)". Genome Res. 14 (10B): 2121–7. doi:10.1101/gr.2596504. PMC 528928 . PMID 15489334.
Gray SG, Iglesias AH, Lizcano F, et al. (2005). "Functional characterization of JMJD2A, a histone deacetylase- and retinoblastoma-binding protein". J. Biol. Chem. 280 (31): 28507–18. doi: 10.1074/jbc.M413687200 . PMID 15927959.
Whetstine JR, Nottke A, Lan F, et al. (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. S2CID 14461740.
Katoh Y, Katoh M (2007). "Comparative integromics on JMJD2A, JMJD2B and JMJD2C: preferential expression of JMJD2C in undifferentiated ES cells". Int. J. Mol. Med. 20 (2): 269–73. doi: 10.3892/ijmm.20.2.269 . PMID 17611647.
Deng P, Yuan Q, Cheng Y, et al. (2021). "Loss of KDM4B exacerbates bone-fat imbalance and mesenchymal stromal cell exhaustion in skeletal aging". Cell Stem Cell. 28 (6): 1057–1073.e7. doi:10.1016/j.stem.2021.01.010. PMC 8178178 . PMID 33571444.

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[refGRCh38Ensembl-1] 1 2 3 GRCh38: Ensembl release 89: ENSG00000127663 - Ensembl, May 2017

[refGRCm38Ensembl-2] 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000024201 - Ensembl, May 2017

[3] "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.

[4] "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.

[pmid10048485-5] Nagase T, Ishikawa K, Suyama M, Kikuno R, Hirosawa M, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O (May 1999). "Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Res. 5 (6): 355–64. doi: 10.1093/dnares/5.6.355 . PMID 10048485.

[pmid15138608-6] Katoh M, Katoh M (May 2004). "Identification and characterization of JMJD2 family genes in silico". Int J Oncol. 24 (6): 1623–8. doi:10.3892/ijo.25.3.759. PMID 15138608.

[entrez-7] "Entrez Gene: JMJD2B jumonji domain containing 2B".

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v t e Oxidoreductases: dioxygenases, including steroid hydroxylases (EC 1.14)
1.14.11: 2-oxoglutarate	Prolyl hydroxylase HIF prolyl-hydroxylase EGLN1 EGLN2 EGLN3 P4HTM Lysyl hydroxylase AlkB ALKBH1 FTO
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 14α-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 Ecdysone 20-monooxygenase Deoxyhypusine monooxygenase

v t e Enzymes
Activity	Active site Binding site Catalytic triad Oxyanion hole Enzyme promiscuity Diffusion-limited enzyme Coenzyme Cofactor Enzyme catalysis
Regulation	Allosteric regulation Cooperativity Enzyme inhibitor Enzyme activator
Classification	EC number Enzyme superfamily Enzyme family List of enzymes
Kinetics	Enzyme kinetics Eadie–Hofstee diagram Hanes–Woolf plot Lineweaver–Burk plot Michaelis–Menten kinetics
Types	EC1 Oxidoreductases (list) EC2 Transferases (list) EC3 Hydrolases (list) EC4 Lyases (list) EC5 Isomerases (list) EC6 Ligases (list) EC7 Translocases (list)

KDM4B

Related Research Articles

References

Further reading