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PDBsum entry 1pk3

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protein ligands Protein-protein interface(s) links
Transcription repression PDB id
1pk3
Jmol
Contents
Protein chains
76 a.a. *
68 a.a. *
Ligands
BME ×3
Waters ×146
* Residue conservation analysis
PDB id:
1pk3
Name: Transcription repression
Title: Scm sam domain
Structure: Sex comb on midleg cg9495-pa. Chain: a, b, c. Fragment: sequence database residue 795-871, sam domain of scm. Synonym: scm. Engineered: yes. Mutation: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: scm. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.85Å     R-factor:   0.215     R-free:   0.231
Authors: C.A.Kim,M.R.Sawaya,D.Cascio,W.Kim,J.U.Bowie
Key ref:
C.A.Kim et al. (2005). Structural organization of a Sex-comb-on-midleg/polyhomeotic copolymer. J Biol Chem, 280, 27769-27775. PubMed id: 15905166 DOI: 10.1074/jbc.M503055200
Date:
04-Jun-03     Release date:   15-Feb-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9VHA0  (SCM_DROME) -  Polycomb protein Scm
Seq:
Struc:
 
Seq:
Struc:
877 a.a.
76 a.a.*
Protein chain
Pfam   ArchSchema ?
Q9VHA0  (SCM_DROME) -  Polycomb protein Scm
Seq:
Struc:
 
Seq:
Struc:
877 a.a.
68 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 

 
DOI no: 10.1074/jbc.M503055200 J Biol Chem 280:27769-27775 (2005)
PubMed id: 15905166  
 
 
Structural organization of a Sex-comb-on-midleg/polyhomeotic copolymer.
C.A.Kim, M.R.Sawaya, D.Cascio, W.Kim, J.U.Bowie.
 
  ABSTRACT  
 
The polycomb group proteins are required for the stable maintenance of gene repression patterns established during development. They function as part of large multiprotein complexes created via a multitude of protein-protein interaction domains. Here we examine the interaction between the SAM domains of the polycomb group proteins polyhomeotic (Ph) and Sex-comb-on-midleg (Scm). Previously we showed that Ph-SAM polymerizes as a helical structure. We find that Scm-SAM also polymerizes, and a crystal structure reveals an architecture similar to the Ph-SAM polymer. These results suggest that Ph-SAM and Scm-SAM form a copolymer. Binding affinity measurements between Scm-SAM and Ph-SAM subunits in different orientations indicate a preference for the formation of a single junction copolymer. To provide a model of the copolymer, we determined the structure of the Ph-SAM/Scm-SAM junction. Similar binding modes are observed in both homo- and heterocomplex formation with minimal change in helix axis direction at the polymer joint. The copolymer model suggests that polymeric Scm complexes could extend beyond the local domains of polymeric Ph complexes on chromatin, possibly playing a role in long range repression.
 
  Selected figure(s)  
 
Figure 2.
FIG. 2. Ph- and Scm-SAM interactions. a, GST pull-down assay. The top bands corresponds to the GST-fused SAM domains, which are identified on the top panel above each lane. The non-fused SAM domains are indicated by the lower panel. The mutations are listed by their numbered locations where the residue was mutated to Arg. For example, Scm5261 would be the double mutant of L52R and Y61R. Ph5156 and Scm5261 are ML surface mutations and Ph65 and Scm66 are EH surface mutations. Possible binding interactions for the various combinations are illustrated for each lane indicated by the arrows. Scm- and Ph-SAM are illustrated as gray and white objects, respectively, and mutations are indicated by the circled X. b, binding affinity of hetero-SAM domain interactions. The surface plasmon resonance data are shown for the indicated hetero-SAM domain binding orientations that confer a positive binding signal in a (lanes 2 and 3). The fitted curves for the binding reaction are overlaid on the actual data. The observed rate constants and the calculated dissociation constant derived from the rate constants are shown. c, the binding affinities suggest preference for the formation of a single junction copolymer. A nucleated hetero-SAM dimeric complex (K[d] = 54 nM, Fig. 2b) is shown at the left. The two possible ends where either the Ph-SAM or Scm-SAM could bind are indicated with the corresponding dissociation constants for each. Scm-SAM would preferentially bind on the left (to a prior Scm-SAM) and Ph-SAM would preferentially bind on the right (to a prior Ph-SAM). The result of the favorable binding reactions is shown in the middle along with the possible binding modes for additional SAM domains. The right panel shows the expected result of further co-polymerization.
Figure 4.
FIG. 4. Three-dimensional model of the copolymer structure. The model was created from three crystal structures. The individual polymer structures were aligned over their respective SAM domains in the complex structure.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 27769-27775) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20048052 J.Zhang, T.G.Graham, P.Vivekanand, L.Cote, M.Cetera, and I.Rebay (2010).
Sterile alpha motif domain-mediated self-association plays an essential role in modulating the activity of the Drosophila ETS family transcriptional repressor Yan.
  Mol Cell Biol, 30, 1158-1170.  
20346678 L.Morey, and K.Helin (2010).
Polycomb group protein-mediated repression of transcription.
  Trends Biochem Sci, 35, 323-332.  
18618697 A.Bhunia, P.N.Domadia, H.Mohanram, and S.Bhattacharjya (2009).
NMR structural studies of the Ste11 SAM domain in the dodecyl phosphocholine micelle.
  Proteins, 74, 328-343.  
18831011 A.D.Meruelo, and J.U.Bowie (2009).
Identifying polymer-forming SAM domains.
  Proteins, 74, 1-5.  
19494831 C.Grimm, R.Matos, N.Ly-Hartig, U.Steuerwald, D.Lindner, V.Rybin, J.Müller, and C.W.Müller (2009).
Molecular recognition of histone lysine methylation by the Polycomb group repressor dSfmbt.
  EMBO J, 28, 1965-1977.
PDB code: 3h6z
19345089 J.Müller, and P.Verrijzer (2009).
Biochemical mechanisms of gene regulation by polycomb group protein complexes.
  Curr Opin Genet Dev, 19, 150-158.  
18287031 T.Rajakulendran, M.Sahmi, I.Kurinov, M.Tyers, M.Therrien, and F.Sicheri (2008).
CNK and HYP form a discrete dimer by their SAM domains to mediate RAF kinase signaling.
  Proc Natl Acad Sci U S A, 105, 2836-2841.
PDB codes: 3bs5 3bs7
17519008 J.J.Kwan, and L.W.Donaldson (2007).
The NMR structure of the murine DLC2 SAM domain reveals a variant fold that is similar to a four-helix bundle.
  BMC Struct Biol, 7, 34.  
17409073 M.M.Harrison, X.Lu, and H.R.Horvitz (2007).
LIN-61, one of two Caenorhabditis elegans malignant-brain-tumor-repeat-containing proteins, acts with the DRM and NuRD-like protein complexes in vulval development but not in certain other biological processes.
  Genetics, 176, 255-271.  
16793273 E.D.Gundelfinger, T.M.Boeckers, M.K.Baron, and J.U.Bowie (2006).
A role for zinc in postsynaptic density asSAMbly and plasticity?
  Trends Biochem Sci, 31, 366-373.  
16362034 F.Qiao, B.Harada, H.Song, J.Whitelegge, A.J.Courey, and J.U.Bowie (2006).
Mae inhibits Pointed-P2 transcriptional activity by blocking its MAPK docking site.
  EMBO J, 25, 70-79.  
17125150 R.L.Rich, and D.G.Myszka (2006).
Survey of the year 2005 commercial optical biosensor literature.
  J Mol Recognit, 19, 478-534.  
16429151 T.Aviv, Z.Lin, G.Ben-Ari, C.A.Smibert, and F.Sicheri (2006).
Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p.
  Nat Struct Mol Biol, 13, 168-176.
PDB code: 2f8k
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.