Pages 1–13 2fmm Evolutionary trace report by report maker June 27, 2010 4 Notes on using trace results 11 4.1 Coverage 11 4.2 Known substitutions 11 4.3 Surface 11 4.4 Number of contacts 11 4.5 Annotation 11 4.6 Mutation suggestions 11 5 Appendix 11 5.1 File formats 11 5.2 Color schemes used 12 5.3 Credits 12 5.3.1 Alistat 12 5.3.2 CE 12 5.3.3 DSSP 12 5.3.4 HSSP 12 5.3.5 LaTex 12 5.3.6 Muscle 12 5.3.7 Pymol 12 5.4 Note about ET Viewer 12 5.5 Citing this work 12 CONTENTS 5.6 About report maker 13 5.7 Attachments 13 1 Introduction 1 2 Chain 2fmmA 1 1 INTRODUCTION 2.1 Q6E6J7 overview 1 From the original Protein Data Bank entry (PDB id 2fmm): 2.2 Multiple sequence alignment for 2fmmA 1 Title: Crystal structure of emsy-hp1 complex 2.3 Residue ranking in 2fmmA 1 Compound: Mol id: 1; molecule: protein emsy; chain: e; frag- 2.4 Top ranking residues in 2fmmA and their position ment: n-terminal domain; engineered: yes; mol id: 2; molecule: on the structure 1 chromobox protein homolog 1; chain: a, b, c, d; fragment: chromo 2.4.1 Clustering of residues at 25% coverage. 1 shadow domain; synonym: heterochromatin protein 1 homolog beta, 2.4.2 Overlap with known functional surfaces at hp1 beta, modifier 1 protein, m31, heterochromatin protein p25, 25% coverage. 2 hp1hsbeta, p25beta; engineered: yes 2.4.3 Possible novel functional surfaces at 25% Organism, scientific name: Homo Sapiens; coverage. 5 2fmm contains unique chains 2fmmA (68 residues) and 2fmmE (118 residues) 2fmmD, 2fmmC, and 2fmmB are homologues of chain 3 Chain2fmmE 6 2fmmA. 3.1 Q7Z589 overview 6 3.2 Multiple sequence alignment for 2fmmE 7 2 CHAIN 2FMMA 3.3 Residue ranking in 2fmmE 7 3.4 Top ranking residues in 2fmmE and their position on 2.1 Q6E6J7 overview the structure 7 From SwissProt, id Q6E6J7, 100% identical to 2fmmA: 3.4.1 Clustering of residues at 25% coverage. 7 Description: Heterochromatin protein 1 beta. 3.4.2 Overlap with known functional surfaces at Organism, scientific name: Cricetulus griseus (Chinese hamster). 25% coverage. 8 Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Verte- 3.4.3 Possible novel functional surfaces at 25% brata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; coverage. 10 Rodentia; Sciurognathi; Muridae; Cricetinae; Cricetulus. 1 Lichtarge lab 2006 Fig. 1. Residues 108-175 in 2fmmA colored by their relative importance. (See Appendix, Fig.17, for the coloring scheme.) 2.2 Multiple sequence alignment for 2fmmA For the chain 2fmmA, the alignment 2fmmA.msf (attached) with 69 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 2fmmA.msf. Its statistics, from the alistat program are the following: Format: MSF Number of sequences: 69 Total number of residues: 4331 Smallest: 22 Largest: 68 Fig. 2. Residues in 2fmmA, colored by their relative importance. Clockwise: Average length: 62.8 front, back, top and bottom views. Alignment length: 68 Average identity: 53% Most related pair: 99% Most unrelated pair: 8% Most distant seq: 38% Furthermore, <1% of residues show as conserved in this ali- gnment. The alignment consists of 44% eukaryotic ( 26% vertebrata, 11% arthropoda) sequences. (Descriptions of some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 2fmmA.descr. 2.3 Residue ranking in 2fmmA The 2fmmA sequence is shown in Fig. 1, with each residue colored according to its estimated importance. The full listing of residues in 2fmmA can be found in the file called 2fmmA.ranks sorted in the attachment. 2.4 Top ranking residues in 2fmmA 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 2fmmA colored by their importance: bright red and yellow indicate more conser- Fig. 3. Residues in 2fmmA, colored according to the cluster they belong to: ved/important residues (see Appendix for the coloring scheme). A red, followed by blue and yellow are the largest clusters (see Appendix for Pymol script for producing this figure can be found in the attachment. the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. 2.4.1 Clustering of residues at 25% coverage. Fig. 3 shows the top 25% of all residues, this time colored according to clusters they Table 1. belong to. The clusters in Fig.3 are composed of the residues listed cluster size member in Table 1. color residues continued in next column 2 Table 1. continued cluster size member color residues red 15 112,113,122,124,134,135,146 147,149,157,160,161,163,164 165 Table 1. Clusters of top ranking residues in 2fmmA. 2.4.2 Overlap with known functional surfaces at 25% coverage. The name of the ligand is composed of the source PDB identifier and the heteroatom name used in that file. Interface with 2fmmB.By analogy with 2fmmC – 2fmmB inter- face. Table 2 lists the top 25% of residues at the interface with 2fmmB. The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 4.6). Table 2. res type subst’s cvg noc/ dist (%) bb (A˚ ) 135 L L(91) 0.09 18/0 3.63 .(1) Fig. 4. Residues in 2fmmA, at the interface with 2fmmB, colored by their W(2) relative importance. 2fmmB is shown in backbone representation (See Appen- F(1) dix for the coloring scheme for the protein chain 2fmmA.) N(1) I(1) 146 L L(78) 0.18 8/0 4.23 Table 4. I(4) res type subst’s cvg noc/ dist M(8) (%) bb (A˚ ) V(4) 165 E E(84) 0.12 2/2 4.23 A(1) Q(8) Q(1) .(4) .(1) W(1) K(1) Table 2. The top 25% of residues in 2fmmA at the interface with 2fmmB. (Field names: res: residue number in the PDB entry; type: amino acid type; Table 4. The top 25% of residues in 2fmmA at the interface with 2fmmC. substs: substitutions seen in the alignment; with the percentage of each type (Field names: res: residue number in the PDB entry; type: amino acid type; in the bracket; noc/bb: number of contacts with the ligand, with the number of substs: substitutions seen in the alignment; with the percentage of each type contacts realized through backbone atoms given in the bracket; dist: distance in the bracket; noc/bb: number of contacts with the ligand, with the number of of closest apporach to the ligand. ) contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) Table 3. res type disruptive mutations Table 5. 135 L (R)(Y)(T)(EH) res type disruptive 146 L (Y)(R)(H)(T) mutations 165 E (FWH)(YCG)(VA)(T) Table 3. List of disruptive mutations for the top 25% of residues in 2fmmA, that are at the interface with 2fmmB. Table 5. List of disruptive mutations for the top 25% of residues in 2fmmA, that are at the interface with 2fmmC. Figure 4 shows residues in 2fmmA colored by their importance, at the interface with 2fmmB. Figure 5 shows residues in 2fmmA colored by their importance, at Interface with 2fmmC.Table 4 lists the top 25% of residues at the interface with 2fmmC. the interface with 2fmmC. The following table (Table 5) suggests Interface with 2fmmD.By analogy with 2fmmC – 2fmmD inter- possible disruptive replacements for these residues (see Section 4.6). face. Table 6 lists the top 25% of residues at the interface with 2fmmD. The following table (Table 7) suggests possible disruptive replacements for these residues (see Section 4.6). 3 Table 6. res type subst’s cvg noc/ dist (%) bb (A˚ ) 157 P P(95) 0.01 16/8 3.68 .(2) S(1) 161 I I(94) 0.03 48/7 3.54 .(4) L(1) 165 E E(84) 0.12 28/9 3.28 Q(8) .(4) W(1) K(1) 164 Y Y(88) 0.15 68/7 3.35 .(4) F(5) C(1) 160 V V(82) 0.16 7/0 4.25 L(8) .(4) I(1) Fig. 5. Residues in 2fmmA, at the interface with 2fmmC, colored by their M(1) relative importance. 2fmmC is shown in backbone representation (See Appen- D(1) dix for the coloring scheme for the protein chain 2fmmA.) 126 T T(79) 0.23 8/8 4.08 S(8) F(2) .(2) Y(1) C(2) V(1) 149 A A(69) 0.25 1/0 4.90 S(24) N(1) M(1) L(1) .(1) Table 6. The top 25% of residues in 2fmmA at the interface with 2fmmD. (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. ) Table 7. res type disruptive mutations 157 P (R)(Y)(H)(T) 161 I (Y)(R)(T)(H) 165 E (FWH)(YCG)(VA)(T) 164 Y (K)(Q)(M)(E) 160 V (YR)(KH)(E)(Q) 126 T (K)(R)(Q)(M) 149 A (Y)(R)(H)(KE) continued in next column 4 Table 7.