Pages 1–6 2czy Evolutionary trace report by report maker July 31, 2009 4.3.1 Alistat 5 4.3.2 CE 6 4.3.3 DSSP 6 4.3.4 HSSP 6 4.3.5 LaTex 6 4.3.6 Muscle 6 4.3.7 Pymol 6 4.4 Note about ET Viewer 6 4.5 Citing this work 6 4.6 About report maker 6 4.7 Attachments 6 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 2czy): Title: Solution structure of the nrsf/rest-msin3b pah1 complex Compound: Mol id: 1; molecule: paired amphipathic helix protein sin3b; chain: a; fragment: pah1 domain (residues 31-107); synonym: sin3b, transcriptional corepressor sin3b, histone deacetylase complex subunit sin3b; engineered: yes; mol id: 2; molecule: transcription factor rest (version 3); chain: b; fragment: sin3 interaction domain (residues 43-57); synonym: nrsf/rest; engineered: yes CONTENTS Organism, scientific name: Mus Musculus; 2czy contains a single unique chain 2czyA (77 residues long). 1 Introduction 1 Chain 2czyB is too short (15 residues) to permit statistically signi- ficant analysis, and was treated as a peptide ligand. This is an 2 Chain 2czyA 1 NMR-determined structure – in this report the first model in the file 2.1 Q62141 overview 1 was used. 2.2 Multiple sequence alignment for 2czyA 1 2.3 Residue ranking in 2czyA 2 2 CHAIN 2CZYA 2.4 Top ranking residues in 2czyA and their position on 2.1 Q62141 overview the structure 2 2.4.1 Clustering of residues at 25% coverage. 2 From SwissProt, id Q62141, 100% identical to 2czyA: 2.4.2 Overlap with known functional surfaces at Description: Paired amphipathic helix protein Sin3b (Transcriptio- 25% coverage. 3 nal corepressor Sin3b) (Histone deacetylase complex subunit Sin3b). 2.4.3 Possible novel functional surfaces at 25% Organism, scientific name: Mus musculus (Mouse). coverage. 4 Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Verte- brata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; 3 Notes on using trace results 4 Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus. 3.1 Coverage 4 Function: Acts as a transcriptional repressor. Interacts with MXI1 3.2 Known substitutions 4 to repress MYC responsive genes and antagonize MYC oncoge- 3.3 Surface 5 nic activities. Interacts with MAD-MAX heterodimers by binding 3.4 Number of contacts 5 to MAD. The heterodimer then represses transcription by tethering 3.5 Annotation 5 SIN3B to DNA. Also forms a complex with FOXK1 which represses 3.6 Mutation suggestions 5 transcription. Subunit: Interacts with HCFC1 (By similarity). Interacts with 4 Appendix 5 FOXK1/MNF, MXI1, MAD, NCOR1 and SAP30. Interaction with 4.1 File formats 5 SDS3 enhances the interaction with HDAC1 to form a complex. 4.2 Color schemes used 5 Subcellular location: Nuclear. 4.3 Credits 5 Alternative products: 1 Lichtarge lab 2006 2.4 Top ranking residues in 2czyA and their position on the structure In the following we consider residues ranking among top 25% of residues in the protein . Figure 2 shows residues in 2czyA colored by their importance: bright red and yellow indicate more conser- Fig. 1. Residues 31-107 in 2czyA colored by their relative importance. (See ved/important residues (see Appendix for the coloring scheme). A Appendix, Fig.6, for the coloring scheme.) Pymol script for producing this figure can be found in the attachment. Event=Alternative splicing; Named isoforms=4; Name=4; IsoId=Q62141-4; Sequence=Displayed; Note=No experimental con- firmation available; Name=1; IsoId=Q62141-1; Sequence=VSP 014187; Name=2; IsoId=Q62141-2; Sequence=VSP 008225, VSP 008226, VSP 014187; Name=3; IsoId=Q62141-3; Sequence=VSP 008227, VSP 008228, VSP 014187; Note=No experimental confir- mation available; Similarity: Contains 3 PAH (paired amphipathic helix) repeats. About: This Swiss-Prot entry is copyright. It is produced through a collaboration between the Swiss Institute of Bioinformatics and the EMBL outstation - the European Bioinformatics Institute. There are no restrictions on its use as long as its content is in no way modified and this statement is not removed. 2.2 Multiple sequence alignment for 2czyA For the chain 2czyA, the alignment 2czyA.msf (attached) with 107 sequences was used. The alignment was downloaded from the HSSP database, and fragments shorter than 75% of the query as well as duplicate sequences were removed. It can be found in the attachment to this report, under the name of 2czyA.msf. Its statistics, from the alistat program are the following: Fig. 2. Residues in 2czyA, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 107 Total number of residues: 7747 Smallest: 63 2.4.1 Clustering of residues at 25% coverage. Fig. 3 shows the Largest: 77 top 25% of all residues, this time colored according to clusters they Average length: 72.4 belong to. The clusters in Fig.3 are composed of the residues listed Alignment length: 77 in Table 1. Average identity: 49% Most related pair: 99% Table 1. Most unrelated pair: 9% cluster size member Most distant seq: 32% color residues red 19 37,40,44,45,48,55,58,62,66 75,79,82,83,89,92,93,96,97 Furthermore, <1% of residues show as conserved in this ali- 98 gnment. The alignment consists of 42% eukaryotic ( 6% vertebrata, 1% Table 1. Clusters of top ranking residues in 2czyA. arthropoda, 11% fungi, 19% plantae) sequences. (Descriptions of some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 2.4.2 Overlap with known functional surfaces at 25% coverage. 2czyA.descr. The name of the ligand is composed of the source PDB identifier and the heteroatom name used in that file. 2.3 Residue ranking in 2czyA Interface with the peptide 2czyB. Table 2 lists the top 25% of residues at the interface with 2czyB. The following table (Table The 2czyA sequence is shown in Fig. 1, with each residue colored 3) suggests possible disruptive replacements for these residues (see according to its estimated importance. The full listing of residues Section 3.6). in 2czyA can be found in the file called 2czyA.ranks sorted in the attachment. 2 Table 2. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) L(1) R(1) S(1) 66 K K(79) 0.22 300/7 2.07 S(1) Q(5) R(7)A G(1)YNC 40 Y Y(85) 0.25 14/0 4.08 F(11) .(1)A Table 2. The top 25% of residues in 2czyA at the interface with 2czyB. (Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each type in the bracket; noc/bb: number of contacts with the ligand, with the number of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) Fig. 3. Residues in 2czyA, colored according to the cluster they belong to: Table 3. red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The res type disruptive corresponding Pymol script is attached. mutations 97 L (R)(Y)(H)(K) 93 F (KE)(T)(QDR)(SCG) Table 2. 37 A (R)(K)(E)(Q) res type subst’s cvg noc/ dist 75 V (R)(K)(E)(Y) (%) bb (A˚ ) 96 F (K)(E)(TQ)(DR) 97 L L(94) 0.04 32/2 3.17 58 F (KE)(T)(DR)(Q) V(2)T 62 M (Y)(T)(HR)(SCG) I(1) 98 P (Y)(R)(H)(T) 93 F F(96) 0.05 80/0 2.00 66 K (Y)(FW)(T)(VAHD) L(3) 40 Y (K)(Q)(EM)(NR) 37 A A(94)PC 0.08 113/18 2.80 GY.(1) Table 3. List of disruptive mutations for the top 25% of residues in 75 V V(89) 0.12 72/1 2.29 2czyA, that are at the interface with 2czyB. C(1) A(3) Figure 4 shows residues in 2czyA colored by their importance, at the L(1)YMG interface with 2czyB. 96 F F(93) 0.13 152/20 2.58 L(1) 2.4.3 Possible novel functional surfaces at 25% coverage. One I(1) group of residues is conserved on the 2czyA surface, away from (or Y(1)W susbtantially larger than) other functional sites and interfaces reco- 58 F F(93) 0.14 20/0 2.98 gnizable in PDB entry 2czy. It is shown in Fig. 5. The residues M(1) belonging to this surface ”patch” are listed in Table 4, while Table L(1)VIW 5 suggests possible disruptive replacements for these residues (see 62 M M(83) 0.17 189/22 1.98 Section 3.6). L(14)IF Table 4. V res type substitutions(%) cvg 98 P P(92) 0.18 16/0 4.21 89 L L(98)P(1) 0.01 .(1) 55 Y Y(97).F(1) 0.03 continued in next column 97 L L(94)V(2)TI(1) 0.04 93 F F(96)L(3) 0.05 continued in next column 3 Table 4. continued res type substitutions(%) cvg L(1)YMG 96 F F(93)L(1)I(1) 0.13 Y(1)W 58 F F(93)M(1)L(1)VI 0.14 W 62 M M(83)L(14)IFV 0.17 98 P P(92).(1)L(1) 0.18 R(1)S(1) 66 K K(79)S(1)Q(5) 0.22 R(7)AG(1)YNC 92 G G(84)A(1)D(2) 0.23 R(2)E(6)VT 40 Y Y(85)F(11).(1)A 0.25 Table 4.