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2l89

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Solution structure of Pdp1 PWWP domain reveals its unique binding sites for methylated H4K20 and DNA

Structural highlights

2l89 is a 1 chain structure with sequence from Schizosaccharomyces pombe. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PDP1_SCHPO Necessary for DNA damage checkpoint activation. Required for the association of set9 with chromatin and subsequent methylation of H4K20. Associates with H4K20me1 to increase the concentration of set9 on chromatin to perform H4K20me3. H4K20me3 is mainly enriched at heterochromatin and is required for proper heterochromatin assembly.^[1]

Publication Abstract from PubMed

Methylation of H4K20 plays an important role in the regulation of diverse cellular processes. In fission yeast, all the three states of H4K20 methylation are catalyzed by Set9. Pdp1 is a PWWP domain-containing protein, which associates with Set9 to regulate its chromatin localization and methyltransferase activity towards H4K20. The structure of Pdp1 PWWP domain, which is the first identified PWWP domain that binds to methyl-lysine at H4K20 site, was determined by solution NMR in the present study. Pdp1 PWWP domain adopts a classical PWWP fold, with a 5-strand antiparallel beta-barrel followed by three alpha-helices. However, it differs significantly from other PWWP domains in some structural aspects that account in part for its molecular recognition. Moreover, we revealed a unique binding pattern of the PWWP domain in that the PWWP domain of Pdp1 bound not only to H4K20me3 but also to dsDNA via an aromatic cage and a positively charged area respectively. Electrophoretic Mobility Shift Assay (EMSA) illustrated the ability of Pdp1 PWWP domain to bind the nucleosome core particle and further mutagenesis experiments indicated the crucial role of this binding activity in histone H4K20 di- and tri- methylation in yeast cells. Our study may shed light on a novel mechanism of histone methylation regulation by the PWWP domain.

Solution structure of Pdp1 PWWP domain reveals its unique binding sites for methylated H4K20 and DNA.,Qiu Y, Zhang W, Zhao C, Wang Y, Wang W, Zhang J, Zhang Z, Li G, Shi Y, Tu X, Wu J Biochem J. 2011 Dec 13. PMID:22150589^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wang Y, Reddy B, Thompson J, Wang H, Noma K, Yates JR 3rd, Jia S. Regulation of Set9-mediated H4K20 methylation by a PWWP domain protein. Mol Cell. 2009 Feb 27;33(4):428-37. doi: 10.1016/j.molcel.2009.02.002. PMID:19250904 doi:http://dx.doi.org/10.1016/j.molcel.2009.02.002
↑ Qiu Y, Zhang W, Zhao C, Wang Y, Wang W, Zhang J, Zhang Z, Li G, Shi Y, Tu X, Wu J. Solution structure of Pdp1 PWWP domain reveals its unique binding sites for methylated H4K20 and DNA. Biochem J. 2011 Dec 13. PMID:22150589 doi:http://dx.doi.org/10.1042/BJ20111885