dbPTM

H33_ARATH - PTM Information in dbPTM

Basic Information of Protein

Overview of Protein Modification Sites with Functional and Structural Information
UniProt ID	H33_ARATH
UniProt AC	P59169
Protein Name	Histone H3.3
Gene Name	HTR4
Organism	Arabidopsis thaliana (Mouse-ear cress).
Sequence Length	136
Subcellular Localization	Nucleus . Chromosome . Nucleus, nucleolus . Localized at rDNA loci in the nucleolus.
Protein Description	Variant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes. Constitutes the predominant form of histone H3 in non-dividing cells and is incorporated into chromatin independently of DNA synthesis. Deposited at sites of nucleosomal displacement throughout transcribed genes, suggesting that it represents an epigenetic imprint of transcriptionally active chromatin. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling..
Protein Sequence	MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Experimental Post-Translational Modification Sites

* ASA = Accessible Surface Area

Locations	Modification	Substrate Peptides & Secondary Structure	ASA (%)	Reference
5	"N6,N6,N6-trimethyllysine"	---MARTKQTARKST ---CCCCCHHHHHCC	39.85	-
5	Methylation	---MARTKQTARKST ---CCCCCHHHHHCC	39.85	14712277
10	"N6,N6,N6-trimethyllysine"	RTKQTARKSTGGKAP CCCHHHHHCCCCCCC	50.32	-
10	Methylation	RTKQTARKSTGGKAP CCCHHHHHCCCCCCC	50.32	12456661
10	Acetylation	RTKQTARKSTGGKAP CCCHHHHHCCCCCCC	50.32	12581305
11	Phosphorylation	TKQTARKSTGGKAPR CCHHHHHCCCCCCCH	27.08	14610360
12	Phosphorylation	KQTARKSTGGKAPRK CHHHHHCCCCCCCHH	53.65	15753571
15	Acetylation	ARKSTGGKAPRKQLA HHHCCCCCCCHHHHH	57.47	17363895
19	Acetylation	TGGKAPRKQLATKAA CCCCCCHHHHHHHHH	48.91	12581305
19	Methylation	TGGKAPRKQLATKAA CCCCCCHHHHHHHHH	48.91	15598823
24	Acetylation	PRKQLATKAARKSAP CHHHHHHHHHHHHCC	34.15	15598823
24	Methylation	PRKQLATKAARKSAP CHHHHHHHHHHHHCC	34.15	15598823
28	"N6,N6,N6-trimethyllysine"	LATKAARKSAPTTGG HHHHHHHHHCCCCCC	46.36	-
28	Methylation	LATKAARKSAPTTGG HHHHHHHHHCCCCCC	46.36	24626927
29	Phosphorylation	ATKAARKSAPTTGGV HHHHHHHHCCCCCCC	33.65	14610360
37	"N6,N6,N6-trimethyllysine"	APTTGGVKKPHRYRP CCCCCCCCCCCCCCC	64.95	-
37	Methylation	APTTGGVKKPHRYRP CCCCCCCCCCCCCCC	64.95	16299497

Upstream regulatory proteins (kinases for phosphorylation sites, E3 ubiquitin ligases of ubiquitination sites, ...)

Modified Location	Modified Residue	Modification	Type of Upstream Proteins	Gene Name of Upstream Proteins	UniProt AC of Upstream Proteins	Sources
Oops, there are no upstream regulatory protein records of H33_ARATH !!

Functions of PTM Sites

Modified Location	Modified Residue	Modification	Function	Reference
32	T	Methylation		17174094
Monomethylation at H3K27me1 by ATXR5/6 is inhibited by the presence of Thr-32.

Disease-associated PTM Sites based on SAP

* Distance = the distance between SAP position and PTM sites.

Modified Location	Modification	Variant Position (Distance <= 10)	Residue Change	SAP	Related Disease	Reference
Oops, there are no SNP-PTM records of H33_ARATH !!

Protein-Protein Interaction

Interacting Protein	Gene Name	Interaction Type	PPI Reference	Domain-Domain Interactions
HIRA_ARATH	HIRA	physical	25086063

Drug and Disease Associations

Kegg Drug
DrugBank
There are no disease associations of PTM sites.

Regulatory Network of H33_ARATH

Related Literatures of Post-Translational Modification

Acetylation
Reference	PubMed
"SKB1-mediated symmetric dimethylation of histone H4R3 controlsflowering time in Arabidopsis."; Wang X., Zhang Y., Ma Q., Zhang Z., Xue Y., Bao S., Chong K.; EMBO J. 26:1934-1941(2007). Cited for: ACETYLATION AT LYS-15.	17363895 [Abstract]
"Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance."; Earley K., Lawrence R.J., Pontes O., Reuther R., Enciso A.J.,Silva M., Neves N., Gross M., Viegas W., Pikaard C.S.; Genes Dev. 20:1283-1293(2006). Cited for: ACETYLATION AT LYS-15 BY HAG1, AND DEACETYLATION BY HDA6.	16648464 [Abstract]
"Mass spectrometry analysis of Arabidopsis histone H3 reveals distinctcombinations of post-translational modifications."; Johnson L., Mollah S., Garcia B.A., Muratore T.L., Shabanowitz J.,Hunt D.F., Jacobsen S.E.; Nucleic Acids Res. 32:6511-6518(2004). Cited for: ACETYLATION AT LYS-10; LYS-15; LYS-19 AND LYS-24, ABSENCE OFACETYLATION AT LYS-28 AND LYS-37, METHYLATION AT LYS-5; LYS-10;LYS-19; LYS-24; LYS-28 AND LYS-37, ABSENCE OF METHYLATION AT LYS-15,AND MASS SPECTROMETRY.	15598823 [Abstract]
"Histone modifications in Arabidopsis -- high methylation of H3 lysine9 is dispensable for constitutive heterochromatin."; Jasencakova Z., Soppe W.J.J., Meister A., Gernand D., Turner B.M.,Schubert I.; Plant J. 33:471-480(2003). Cited for: ACETYLATION AT LYS-10 AND LYS-19, AND METHYLATION AT LYS-5 AND LYS-10.	12581305 [Abstract]
Methylation
Reference	PubMed
"Prevention of early flowering by expression of FLOWERING LOCUS Crequires methylation of histone H3 K36."; Zhao Z., Yu Y., Meyer D., Wu C., Shen W.-H.; Nat. Cell Biol. 7:1256-1260(2005). Cited for: METHYLATION AT LYS-37.	16299497 [Abstract]
"Establishment of the vernalization-responsive, winter-annual habit inArabidopsis requires a putative histone H3 methyl transferase."; Kim S.Y., He Y., Jacob Y., Noh Y.-S., Michaels S., Amasino R.; Plant Cell 17:3301-3310(2005). Cited for: METHYLATION AT LYS-5.	16258034 [Abstract]
"Vernalization requires epigenetic silencing of FLC by histonemethylation."; Bastow R., Mylne J.S., Lister C., Lippman Z., Martienssen R.A.,Dean C.; Nature 427:164-167(2004). Cited for: METHYLATION AT LYS-5; LYS-10 AND LYS-28.	14712277 [Abstract]
"Mass spectrometry analysis of Arabidopsis histone H3 reveals distinctcombinations of post-translational modifications."; Johnson L., Mollah S., Garcia B.A., Muratore T.L., Shabanowitz J.,Hunt D.F., Jacobsen S.E.; Nucleic Acids Res. 32:6511-6518(2004). Cited for: ACETYLATION AT LYS-10; LYS-15; LYS-19 AND LYS-24, ABSENCE OFACETYLATION AT LYS-28 AND LYS-37, METHYLATION AT LYS-5; LYS-10;LYS-19; LYS-24; LYS-28 AND LYS-37, ABSENCE OF METHYLATION AT LYS-15,AND MASS SPECTROMETRY.	15598823 [Abstract]
"Dimethylation of histone H3 lysine 9 is a critical mark for DNAmethylation and gene silencing in Arabidopsis thaliana."; Jackson J.P., Johnson L., Jasencakova Z., Zhang X., PerezBurgos L.,Singh P.B., Cheng X., Schubert I., Jenuwein T., Jacobsen S.E.; Chromosoma 112:308-315(2004). Cited for: METHYLATION AT LYS-10.	15014946 [Abstract]
"Histone modifications in Arabidopsis -- high methylation of H3 lysine9 is dispensable for constitutive heterochromatin."; Jasencakova Z., Soppe W.J.J., Meister A., Gernand D., Turner B.M.,Schubert I.; Plant J. 33:471-480(2003). Cited for: ACETYLATION AT LYS-10 AND LYS-19, AND METHYLATION AT LYS-5 AND LYS-10.	12581305 [Abstract]
"DNA methylation controls histone H3 lysine 9 methylation andheterochromatin assembly in Arabidopsis."; Soppe W.J.J., Jasencakova Z., Houben A., Kakutani T., Meister A.,Huang M.S., Jacobsen S.E., Schubert I., Fransz P.F.; EMBO J. 21:6549-6559(2002). Cited for: METHYLATION AT LYS-10.	12456661 [Abstract]
"Whole-genome analysis of histone H3 lysine 27 trimethylation inArabidopsis."; Zhang X., Clarenz O., Cokus S., Bernatavichute Y.V., Pellegrini M.,Goodrich J., Jacobsen S.E.; PLoS Biol. 5:1026-1035(2007). Cited for: METHYLATION AT LYS-28, AND SUBCELLULAR LOCATION.	17439305 [Abstract]
"The PHD finger protein VRN5 functions in the epigenetic silencing ofArabidopsis FLC."; Greb T., Mylne J.S., Crevillen P., Geraldo N., An H., Gendall A.R.,Dean C.; Curr. Biol. 17:73-78(2007). Cited for: ACETYLATION, AND METHYLATION AT LYS-28.	17174094 [Abstract]
Phosphorylation
Reference	PubMed
"Novel phosphorylation of histone H3 at threonine 11 that temporallycorrelates with condensation of mitotic and meiotic chromosomes inplant cells."; Houben A., Demidov D., Rutten T., Scheidtmann K.H.; Cytogenet. Genome Res. 109:148-155(2005). Cited for: PHOSPHORYLATION AT SER-11; THR-12 AND SER-29.	15753571 [Abstract]
"The temporal and spatial pattern of histone H3 phosphorylation atserine 28 and serine 10 is similar in plants but differs between mono-and polycentric chromosomes."; Gernand D., Demidov D., Houben A.; Cytogenet. Genome Res. 101:172-176(2003). Cited for: PHOSPHORYLATION AT SER-11 AND SER-29.	14610360 [Abstract]

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