PDBsum entry 2cu7

Go to PDB code: 
protein links
Transcription PDB id
Protein chain
72 a.a. *
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Solution structure of the sant domain of human kiaa1915 protein
Structure: Kiaa1915 protein. Chain: a. Fragment: sant domain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: kiaa1915. Other_details: cell-free protein synthesis
NMR struc: 20 models
Authors: M.Yoneyama,T.Umehara,K.Saito,N.Tochio,S.Koshiba,M.Inoue, A.Tanaka,T.Kigawa,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
M.Yoneyama et al. (2007). Structural and Functional Differences of SWIRM Domain Subtypes. J Mol Biol, 369, 222-238. PubMed id: 17428495 DOI: 10.1016/j.jmb.2007.03.027
25-May-05     Release date:   25-Nov-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q5VVJ2  (MYSM1_HUMAN) -  Histone H2A deubiquitinase MYSM1
828 a.a.
72 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     chromatin binding     2 terms  


DOI no: 10.1016/j.jmb.2007.03.027 J Mol Biol 369:222-238 (2007)
PubMed id: 17428495  
Structural and Functional Differences of SWIRM Domain Subtypes.
M.Yoneyama, N.Tochio, T.Umehara, S.Koshiba, M.Inoue, T.Yabuki, M.Aoki, E.Seki, T.Matsuda, S.Watanabe, Y.Tomo, Y.Nishimura, T.Harada, T.Terada, M.Shirouzu, Y.Hayashizaki, O.Ohara, A.Tanaka, T.Kigawa, S.Yokoyama.
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.
  Selected figure(s)  
Figure 1.
Figure 1. Schematic representations of the SWIRM domains. The MYSM1/SMARCC2, Ada2, and LSD1-types of the SWIRM family are shown with the representative SWIRM-containing proteins. Blue, yellow, red, light blue, and green indicate the putative zinc finger, SANT, SWIRM, JAMM, and histone demethylase domains, respectively. The amino acid length of each protein is shown on the right.
Figure 2.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 369, 222-238) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20360860 K.M.Evans-Roberts, C.Breuer, M.K.Wall, K.Sugimoto-Shirasu, and A.Maxwell (2010).
Arabidopsis thaliana GYRB3 does not encode a DNA gyrase subunit.
  PLoS One, 5, e9899.  
18936164 A.M.Gamper, J.Kim, and R.G.Roeder (2009).
The STAGA subunit ADA2b is an important regulator of human GCN5 catalysis.
  Mol Cell Biol, 29, 266-280.  
18226187 M.J.Clague, J.M.Coulson, and S.Urbé (2008).
Deciphering histone 2A deubiquitination.
  Genome Biol, 9, 202.  
17656577 F.He, T.Umehara, K.Tsuda, M.Inoue, T.Kigawa, T.Matsuda, T.Yabuki, M.Aoki, E.Seki, T.Terada, M.Shirouzu, A.Tanaka, S.Sugano, Y.Muto, and S.Yokoyama (2007).
Solution structure of the zinc finger HIT domain in protein FON.
  Protein Sci, 16, 1577-1587.
PDB code: 1x4s
17897944 R.Anand, and R.Marmorstein (2007).
Structure and mechanism of lysine-specific demethylase enzymes.
  J Biol Chem, 282, 35425-35429.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.