Pages 1–6 2i0v Evolutionary trace report by report maker September 17, 2008 4.3.1 Alistat 6 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 2i0v): Title: C-fms tyrosine kinase in complex with a quinolone inhibitor Compound: Mol id: 1; molecule: cfms tyrosine kinase; chain: a; fragment: kinase domain; ec: 2.7.10.1; engineered: yes Organism, scientific name: Homo Sapiens; CONTENTS 2i0v contains a single unique chain 2i0vA (303 residues long). 1 Introduction 1 2 Chain 2i0vA 1 2.1 Q4SQ12 overview 1 2 CHAIN 2I0VA 2.2 Multiple sequence alignment for 2i0vA 1 2.1 Q4SQ12 overview 2.3 Residue ranking in 2i0vA 1 From SwissProt, id Q4SQ12, 63% identical to 2i0vA: 2.4 Top ranking residues in 2i0vA and their position on Description: Chromosome 7 SCAF14536, whole genome shotgun the structure 1 sequence. (Fragment). 2.4.1 Clustering of residues at 25% coverage. 2 Organism, scientific name: Tetraodon nigroviridis (Green puffer). 2.4.2 Overlap with known functional surfaces at Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; 25% coverage. 2 Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleo- 2.4.3 Possible novel functional surfaces at 25% stei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; coverage. 3 Tetraodontiformes; Tetradontoidea; Tetraodontidae; Tetraodon. Caution: 3 Notes on using trace results 4 The sequence shown here is derived from an EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry 3.1 Coverage 4 which is preliminary data. 3.2 Known substitutions 5 3.3 Surface 5 3.4 Number of contacts 5 2.2 Multiple sequence alignment for 2i0vA 3.5 Annotation 5 3.6 Mutation suggestions 5 For the chain 2i0vA, the alignment 2i0vA.msf (attached) with 39 sequences was used. The alignment was assembled through combi- 4 Appendix 5 nation of BLAST searching on the UniProt database and alignment 4.1 File formats 5 using Muscle program. It can be found in the attachment to this 4.2 Color schemes used 5 report, under the name of 2i0vA.msf. Its statistics, from the alistat 4.3 Credits 6 program are the following: 1 Lichtarge lab 2006 residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. Fig. 1. Residues 544-763 in 2i0vA colored by their relative importance. (See Appendix, Fig.7, for the coloring scheme.) Fig. 2. Residues 764-916 in 2i0vA colored by their relative importance. (See Appendix, Fig.7, for the coloring scheme.) Fig. 3. Residues in 2i0vA, colored by their relative importance. Clockwise: front, back, top and bottom views. Format: MSF Number of sequences: 39 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Total number of residues: 11319 top 25% of all residues, this time colored according to clusters they Smallest: 231 belong to. The clusters in Fig.4 are composed of the residues listed Largest: 303 in Table 1. Average length: 290.2 Alignment length: 303 Table 1. Average identity: 54% cluster size member Most related pair: 99% color residues Most unrelated pair: 36% red 74 596,614,615,616,617,618,619 Most distant seq: 43% 630,633,643,645,649,650,651 664,669,671,675,679,761,765 766,769,775,776,777,778,780 Furthermore, 11% of residues show as conserved in this alignment. 781,782,783,785,793,794,796 The alignment consists of 94% eukaryotic ( 56% vertebrata, 797,798,799,800,801,809,817 20% arthropoda), and 2% viral sequences. (Descriptions of some 818,820,821,822,823,824,825 sequences were not readily available.) The file containing the 827,836,837,838,839,842,844 sequence descriptions can be found in the attachment, under the name 846,847,848,851,852,855,856 2i0vA.descr. 857,872,874,878,886,889,892 893,900,901,903 2.3 Residue ranking in 2i0vA blue 2 653,658 The 2i0vA sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues Table 1. Clusters of top ranking residues in 2i0vA. in 2i0vA can be found in the file called 2i0vA.ranks sorted in the attachment. 2.4.2 Overlap with known functional surfaces at 25% coverage. 2.4 Top ranking residues in 2i0vA and their position on The name of the ligand is composed of the source PDB identifier the structure and the heteroatom name used in that file. In the following we consider residues ranking among top 25% of resi- 6C3 binding site. Table 2 lists the top 25% of residues at the inter- dues in the protein . Figure 3 shows residues in 2i0vA colored by their face with 2i0v6C31000 (6c3). The following table (Table 3) suggests importance: bright red and yellow indicate more conserved/important possible disruptive replacements for these residues (see Section 3.6). 2 Table 2. res type subst’s cvg noc/ dist (%) bb (A˚ ) 614 A A(100) 0.11 10/3 3.51 616 K K(100) 0.11 9/0 3.16 664 E E(100) 0.11 8/8 3.36 669 G G(100) 0.11 9/9 3.75 785 L L(100) 0.11 30/0 3.40 796 D D(100) 0.11 3/3 3.62 797 F F(100) 0.11 37/5 3.75 801 R R(100) 0.11 9/0 3.90 596 V V(94) 0.18 17/0 3.98 .(5) 800 A A(82) 0.20 16/8 3.17 T(7) S(10) Table 2. The top 25% of residues in 2i0vA at the interface with 6C3.(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 num- ber of contacts realized through backbone atoms given in the bracket; dist: Fig. 4. Residues in 2i0vA, colored according to the cluster they belong to: distance of closest apporach to the ligand. ) red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The corresponding Pymol script is attached. Table 3. res type disruptive mutations 614 A (KYER)(QHD)(N)(FTMW) 616 K (Y)(FTW)(SVCAG)(HD) 664 E (FWH)(YVCARG)(T)(SNKLPI) 669 G (KER)(FQMWHD)(NYLPI)(SVA) 785 L (YR)(TH)(SKECG)(FQWD) 796 D (R)(FWH)(KYVCAG)(TQM) 797 F (KE)(TQD)(SNCRG)(M) 801 R (TD)(SYEVCLAPIG)(FMW)(N) 596 V (KYER)(QHD)(N)(FTMW) 800 A (KR)(E)(Y)(QH) Table 3. List of disruptive mutations for the top 25% of residues in 2i0vA, that are at the interface with 6C3. Figure 5 shows residues in 2i0vA colored by their importance, at the interface with 2i0v6C31000. 2.4.3 Possible novel functional surfaces at 25% coverage. One group of residues is conserved on the 2i0vA surface, away from (or susbtantially larger than) other functional sites and interfaces reco- gnizable in PDB entry 2i0v. It is shown in Fig. 6. The right panel shows (in blue) the rest of the larger cluster this surface belongs to. The residues belonging to this surface ”patch” are listed in Table 4, while Table 5 suggests possible disruptive replacements for these residues (see Section 3.6). Table 4. res type substitutions(%) cvg 614 A A(100) 0.11 616 K K(100) 0.11 continued in next column 3 Table 4. continued res type substitutions(%) cvg 798 G G(100) 0.11 801 R R(100) 0.11 809 Y Y(100) 0.11 821 W W(100) 0.11 825 E E(100) 0.11 836 S S(100) 0.11 837 D D(100) 0.11 839 W W(100) 0.11 846 W W(100) 0.11 847 E E(100) 0.11 649 L L(97)F(2) 0.12 822 M M(97)T(2) 0.12 761 Q Q(92)D(7) 0.14 799 L L(94)F(5) 0.15 878 P P(97).(2) 0.16 893 W W(97).(2) 0.16 619 K K(94)R(2)Q(2) 0.17 857 P P(89)S(2)C(7) 0.17 872 G G(94)A(2)D(2) 0.17 596 V V(94).(5) 0.18 Fig. 5. Residues in 2i0vA, at the interface with 6C3, colored by their relative 650 L L(94)I(5) 0.18 importance. The ligand (6C3) is colored green. Atoms further than 30A˚ away 679 R R(92)N(5)K(2) 0.18 from the geometric center of the ligand, as well as on the line of sight to the 617 M M(84)T(7)R(7) 0.19 ligand were removed. (See Appendix for the coloring scheme for the protein 630 L L(82)F(15)I(2) 0.20 chain 2i0vA.) 800 A A(82)T(7)S(10) 0.20 886 Y Y(94)H(2).(2) 0.20 900 R R(94)K(2).(2) 0.21 901 P P(94)Q(2).(2) 0.21 903 F F(94)Q(2).(2) 0.21 817 L L(89)V(5)M(2) 0.22 F(2) 824 P P(84)I(10)T(5) 0.22 851 L Y(7)L(89)F(2) 0.23 856 Y Y(94)N(5) 0.23 820 K K(82)R(17) 0.24 827 I L(76)I(23) 0.24 618 L V(5)L(84)M(10) 0.25 Fig.