PDBsum entry 2c5z

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protein links
Transcription PDB id
Protein chain
93 a.a. *
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Structure and ctd binding of the set2 sri domain
Structure: Set domain protein 2. Chain: a. Fragment: set2 rpb1 interacting domain, residues 620-719. Engineered: yes. Other_details: residues 1-4 in the construct used for the structure determination are from the expression vector.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 469008.
NMR struc: 10 models
Authors: E.Vojnic,B.Simon,B.D.Strahl,M.Sattler,P.Cramer
Key ref:
E.Vojnic et al. (2006). Structure and carboxyl-terminal domain (CTD) binding of the Set2 SRI domain that couples histone H3 Lys36 methylation to transcription. J Biol Chem, 281, 13-15. PubMed id: 16286474 DOI: 10.1074/jbc.C500423200
03-Nov-05     Release date:   14-Nov-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P46995  (SET2_YEAST) -  Histone-lysine N-methyltransferase, H3 lysine-36 specific
733 a.a.
93 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure

 Enzyme reactions 
   Enzyme class: E.C.  - Histone-lysine N-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N6-methyl-L-lysine-[histone]
+ L-lysine-[histone]
= S-adenosyl-L-homocysteine
+ N(6)-methyl-L-lysine-[histone]
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     chromosome   1 term 
  Biological process     regulation of transcription, DNA-dependent   2 terms 
  Biochemical function     histone-lysine N-methyltransferase activity     1 term  


    Added reference    
DOI no: 10.1074/jbc.C500423200 J Biol Chem 281:13-15 (2006)
PubMed id: 16286474  
Structure and carboxyl-terminal domain (CTD) binding of the Set2 SRI domain that couples histone H3 Lys36 methylation to transcription.
E.Vojnic, B.Simon, B.D.Strahl, M.Sattler, P.Cramer.
During mRNA elongation, the SRI domain of the histone H3 methyltransferase Set2 binds to the phosphorylated carboxyl-terminal domain (CTD) of RNA polymerase II. The solution structure of the yeast Set2 SRI domain reveals a novel CTD-binding fold consisting of a left-handed three-helix bundle. NMR titration shows that the SRI domain binds an Ser2/Ser5-phosphorylated CTD peptide comprising two heptapeptide repeats and three flanking NH2-terminal residues, whereas a single CTD repeat is insufficient for binding. Residues that show strong chemical shift perturbations upon CTD binding cluster in two regions. Both CTD tyrosine side chains contact the SRI domain. One of the tyrosines binds in the region with the strongest chemical shift perturbations, formed by the two NH2-terminal helices. Unexpectedly, the SRI domain fold resembles the structure of an RNA polymerase-interacting domain in bacterial sigma factors (domain sigma2 in sigma70).
  Selected figure(s)  
Figure 2.
FIGURE 2. Surface analysis of the Set2 SRI domain. Surface representation of the SRI domain color-coded according to chemical shift perturbation of backbone NH and side chain NH[2] groups upon binding of the CTD peptide (supplemental Fig. S3A), colored from red to blue for strong to weak perturbations, respectively (A); amino acid conservation among fungal homologues in the alignment of Fig. 1C (B); and electrostatic surface potential (blue and red for positive and negative charges, respectively) (C).
Figure 3.
FIGURE 3. The Set2 SRI domain resembles a domain in bacterial factors. The domain in the factor that resembles the SRI fold is highlighted in green. The PDB codes of the structures are given in parentheses.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 13-15) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21792193 Almeida, A.R.Grosso, F.Koch, R.Fenouil, S.Carvalho, J.Andrade, H.Levezinho, M.Gut, D.Eick, I.Gut, J.C.Andrau, P.Ferrier, and M.Carmo-Fonseca (2011).
Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36.
  Nat Struct Mol Biol, 18, 977-983.  
20572013 R.Alag, I.A.Qureshi, N.Bharatham, J.Shin, J.Lescar, and H.S.Yoon (2010).
NMR and crystallographic structures of the FK506 binding domain of human malarial parasite Plasmodium vivax FKBP35.
  Protein Sci, 19, 1577-1586.
PDB code: 3ihz
20705653 R.Kanagaraj, D.Huehn, A.MacKellar, M.Menigatti, L.Zheng, V.Urban, I.Shevelev, A.L.Greenleaf, and P.Janscak (2010).
RECQ5 helicase associates with the C-terminal repeat domain of RNA polymerase II during productive elongation phase of transcription.
  Nucleic Acids Res, 38, 8131-8140.  
18184581 A.Casañas, A.Navarro, C.Ferrer-Orta, D.González, J.F.Rodríguez, and N.Verdaguer (2008).
Structural insights into the multifunctional protein VP3 of birnaviruses.
  Structure, 16, 29-37.
PDB codes: 2r18 2z7j
18541663 M.L.Youdell, K.O.Kizer, E.Kisseleva-Romanova, S.M.Fuchs, E.Duro, B.D.Strahl, and J.Mellor (2008).
Roles for Ctk1 and Spt6 in regulating the different methylation states of histone H3 lysine 36.
  Mol Cell Biol, 28, 4915-4926.  
19141475 S.M.Yoh, J.S.Lucas, and K.A.Jones (2008).
The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation.
  Genes Dev, 22, 3422-3434.  
17567462 C.Garcia-Ruiz, and J.C.Fernández-Checa (2007).
Redox regulation of hepatocyte apoptosis.
  J Gastroenterol Hepatol, 22, S38-S42.  
18079404 R.D.Chapman, M.Heidemann, T.K.Albert, R.Mailhammer, A.Flatley, M.Meisterernst, E.Kremmer, and D.Eick (2007).
Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7.
  Science, 318, 1780-1782.  
17984971 S.Lall (2007).
Primers on chromatin.
  Nat Struct Mol Biol, 14, 1110-1115.  
16936819 A.Morillon (2006).
Is histone loss a common feature of DNA metabolism regulation?
  Biochem Cell Biol, 84, 450-462.  
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.