PDBsum entry: 1pk1

Transcription repression

PDB id: 1pk1

Contents

Protein chains

68 a.a. *

70 a.a. *

Waters ×193

* Residue conservation analysis

PDB id:

1pk1

Name:

Transcription repression

Title:

Hetero sam domain structure of ph and scm.

Structure:

Polyhomeotic-proximal chromatin protein. Chain: a, c. Fragment: residue 1502-1577, ph sam domain. Engineered: yes. Mutation: yes. Sex comb on midleg cg9495-pa. Chain: b, d. Fragment: residue 795-871, scm sam domain. Engineered: yes.

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: ph-p. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: sex comb on midleg.

Biol. unit:

Monomer (from PQS)

Resolution:

1.80Å R-factor: 0.233 R-free: 0.249

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

Protein chains

P39769  (PHP_DROME) -  Polyhomeotic-proximal chromatin protein

Seq: 1589 a.a.

Struc: 68 a.a.*

Protein chains

Q9VHA0  (SCM_DROME) -  Polycomb protein Scm

Seq: 877 a.a.

Struc: 70 a.a.*

* 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.