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Structural and functional differences of SWIRM domain subtypes.

Yoneyama M, Tochio N, Umehara T, Koshiba S, Inoue M, Yabuki T, Aoki M, Seki E, Matsuda T, Watanabe S, Tomo Y, Nishimura Y, Harada T, Terada T, Shirouzu M, Hayashizaki Y, Ohara O, Tanaka A, Kigawa T, Yokoyama S
J Mol Biol 369 222-38 (2007)
Related entries: 2cuj, 2dce

Cited: 35 times
EuropePMC logo PMID: 17428495

Abstract

SWIRM is a conserved domain found in several chromatin-associated proteins. Based on their sequences, the SWIRM family members can be classified into three subfamilies, which are represented by Swi3, LSD1, and Ada2. Here we report the SWIRM structure of human MYb-like, Swirm and Mpn domain-containing protein-1 (MYSM1). The MYSM1 SWIRM structure forms a compact HTH-related fold comprising five alpha-helices, which best resembles the Swi3 SWIRM structure, among the known SWIRM structures. The MYSM1 and Swi3 SWIRM structures are more similar to the LSD1 structure than the Ada2alpha structure. The SWIRM domains of MYSM1 and LSD1 lacked DNA binding activity, while those of Ada2alpha and the human Swi3 counterpart, SMARCC2, bound DNA. The dissimilarity in the DNA-binding ability of the MYSM1 and SMARCC2 SWIRM domains might be due to a couple of amino acid differences in the last helix. These results indicate that the SWIRM family has indeed diverged into three structural subfamilies (Swi3/MYSM1, LSD1, and Ada2 types), and that the Swi3/MYSM1-type subfamily has further diverged into two functionally distinct groups. We also solved the structure of the SANT domain of MYSM1, and demonstrated that it bound DNA with a similar mode to that of the c-Myb DNA-binding domain.

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  4. Survey of the year 2007 commercial optical biosensor literature. Rich RL, Myszka DG. J Mol Recognit 21 355-400 (2008)
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  1. Control of B cell development by the histone H2A deubiquitinase MYSM1. Jiang XX, Nguyen Q, Chou Y, Wang T, Nandakumar V, Yates P, Jones L, Wang L, Won H, Lee HR, Jung JU, Müschen M, Huang XF, Chen SY. Immunity 35 883-896 (2011)
  2. Epigenetic control of natural killer cell maturation by histone H2A deubiquitinase, MYSM1. Nandakumar V, Chou Y, Zang L, Huang XF, Chen SY. Proc Natl Acad Sci U S A 110 E3927-36 (2013)
  3. The STAGA subunit ADA2b is an important regulator of human GCN5 catalysis. Gamper AM, Kim J, Roeder RG. Mol Cell Biol 29 266-280 (2009)
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  5. Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay. Machol K, Rousseau J, Ehresmann S, Garcia T, Nguyen TTM, Spillmann RC, Sullivan JA, Shashi V, Jiang YH, Stong N, Fiala E, Willing M, Pfundt R, Kleefstra T, Cho MT, McLaughlin H, Rosello Piera M, Orellana C, Martínez F, Caro-Llopis A, Monfort S, Roscioli T, Nixon CY, Buckley MF, Turner A, Jones WD, van Hasselt PM, Hofstede FC, van Gassen KLI, Brooks AS, van Slegtenhorst MA, Lachlan K, Sebastian J, Madan-Khetarpal S, Sonal D, Sakkubai N, Thevenon J, Faivre L, Maurel A, Petrovski S, Krantz ID, Tarpinian JM, Rosenfeld JA, Lee BH, Undiagnosed Diseases Network, Campeau PM. Am J Hum Genet 104 164-178 (2019)
  6. Deubiquitinase MYSM1 Is Essential for Normal Bone Formation and Mesenchymal Stem Cell Differentiation. Li P, Yang YM, Sanchez S, Cui DC, Dang RJ, Wang XY, Lin QX, Wang Y, Wang C, Chen DF, Chen SY, Jiang XX, Wen N. Sci Rep 6 22211 (2016)
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  9. Deubiquitinase MYSM1 Is Essential for Normal Fetal Liver Hematopoiesis and for the Maintenance of Hematopoietic Stem Cells in Adult Bone Marrow. Förster M, Belle JI, Petrov JC, Ryder EJ, Clare S, Nijnik A. Stem Cells Dev 24 1865-1877 (2015)
  10. Involvement of a Toxoplasma gondii chromatin remodeling complex ortholog in developmental regulation. Rooney PJ, Neal LM, Knoll LJ. PLoS One 6 e19570 (2011)
  11. Comparative Analysis of SWIRM Domain-Containing Proteins in Plants. Gao Y, Yang S, Yuan L, Cui Y, Wu K. Comp Funct Genomics 2012 310402 (2012)
  12. MYSM-1 suppresses migration and invasion in renal carcinoma through inhibiting epithelial-mesenchymal transition. Zhou L, Shi L, Guo H, Yao X. Tumour Biol (2015)
  13. Arabidopsis thaliana GYRB3 does not encode a DNA gyrase subunit. Evans-Roberts KM, Breuer C, Wall MK, Sugimoto-Shirasu K, Maxwell A. PLoS One 5 e9899 (2010)
  14. Mysm1 expression in the bone marrow niche is not essential for hematopoietic maintenance. Petrov JC, Nijnik A. Exp Hematol 47 76-82.e3 (2017)
  15. The Lysine Specific Demethylase-1 Negatively Regulates the COL9A1 Gene in Human Articular Chondrocytes. Durand AL, Dufour A, Aubert-Foucher E, Oger-Desfeux C, Pasdeloup M, Lustig S, Servien E, Vaz G, Perrier-Groult E, Mallein-Gerin F, Lafont JE. Int J Mol Sci 21 (2020)
  16. 1H, 15N, and 13C resonance assignments and secondary structure of the SWIRM domain of human BAF155, a chromatin remodeling complex component. Moon S, Shin J, Lee D, Seong RH, Lee W. Mol Cells 36 333-339 (2013)
  17. SMARCC2 mediates the regulation of DKK1 by the transcription factor EGR1 through chromatin remodeling to reduce the proliferative capacity of glioblastoma. Li C, Wang T, Gu J, Qi S, Li J, Chen L, Wu H, Shi L, Song C, Li H, Zhu L, Lu Y, Zhou Q. Cell Death Dis 13 990 (2022)


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