Pages 1–20 1gw9 Evolutionary trace report by report maker January 27, 2010 4.3.1 Alistat 19 4.3.2 CE 19 4.3.3 DSSP 19 4.3.4 HSSP 19 4.3.5 LaTex 19 4.3.6 Muscle 19 4.3.7 Pymol 19 4.4 Note about ET Viewer 19 4.5 Citing this work 19 4.6 About report maker 19 4.7 Attachments 19 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1gw9): Title: Tri-iodide derivative of xylose isomerase from streptomyces rubiginosus Compound: Mol id: 1; molecule: xylose isomerase; chain: a; ec: 5.3.1.5 Organism, scientific name: Streptomyces Rubiginosus 1gw9 contains a single unique chain 1gw9A (385 residues long). CONTENTS 2 CHAIN 1GW9A 1 Introduction 1 2.1 P24300 overview 2 Chain 1gw9A 1 From SwissProt, id P24300, 96% identical to 1gw9A: 2.1 P24300 overview 1 Description: Xylose isomerase (EC 5.3.1.5). 2.2 Multiple sequence alignment for 1gw9A 1 Organism, scientific name: Streptomyces rubiginosus. 2.3 Residue ranking in 1gw9A 1 Taxonomy: Bacteria; Actinobacteria; Actinobacteridae; Actinomy- 2.4 Top ranking residues in 1gw9A and their position on cetales; Streptomycineae; Streptomycetaceae; Streptomyces. the structure 2 Function: Involved in D-xylose catabolism. 2.4.1 Clustering of residues at 25% coverage. 2 Catalytic activity: D-xylose = D-xylulose. 2.4.2 Overlap with known functional surfaces at Cofactor: Binds 2 magnesium ions per subunit (By similarity). 25% coverage. 2 Subunit: Homotetramer. 2.4.3 Possible novel functional surfaces at 25% Subcellular location: Cytoplasmic. coverage. 16 Similarity: Belongs to the xylose isomerase family. Caution: According to the crystallographic study residue 40 could 3 Notes on using trace results 18 be Gln. 3.1 Coverage 18 About: This Swiss-Prot entry is copyright. It is produced through a 3.2 Known substitutions 18 collaboration between the Swiss Institute of Bioinformatics and the 3.3 Surface 18 EMBL outstation - the European Bioinformatics Institute. There are 3.4 Number of contacts 18 no restrictions on its use as long as its content is in no way modified 3.5 Annotation 18 and this statement is not removed. 3.6 Mutation suggestions 18 2.2 Multiple sequence alignment for 1gw9A 4 Appendix 18 For the chain 1gw9A, the alignment 1gw9A.msf (attached) with 27 4.1 File formats 18 sequences was used. The alignment was assembled through combi- 4.2 Color schemes used 18 nation of BLAST searching on the UniProt database and alignment 4.3 Credits 19 using Muscle program. It can be found in the attachment to this 1 Lichtarge lab 2006 2.4 Top ranking residues in 1gw9A and their position on the structure In the following we consider residues ranking among top 25% of residues in the protein . Figure 3 shows residues in 1gw9A colored by their importance: bright red and yellow indicate more conser- ved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. Fig. 1. Residues 2-193 in 1gw9A colored by their relative importance. (See Appendix, Fig.29, for the coloring scheme.) Fig. 2. Residues 194-386 in 1gw9A colored by their relative importance. (See Appendix, Fig.29, for the coloring scheme.) report, under the name of 1gw9A.msf. Its statistics, from the alistat program are the following: Fig. 3. Residues in 1gw9A, colored by their relative importance. Clockwise: front, back, top and bottom views. Format: MSF Number of sequences: 27 Total number of residues: 10273 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Smallest: 371 top 25% of all residues, this time colored according to clusters they Largest: 385 belong to. The clusters in Fig.4 are composed of the residues listed Average length: 380.5 in Table 1. Alignment length: 385 Table 1. Average identity: 44% cluster size member Most related pair: 99% color residues Most unrelated pair: 21% red 79 3,5,10,11,14,16,17,18,46,47 Most distant seq: 67% 52,53,54,55,57,87,88,90,94 102,105,111,134,135,137,138 Furthermore, 9% of residues show as conserved in this alignment. 139,140,141,142,179,181,182 The alignment consists of 11% eukaryotic ( 11% plantae), and 183,184,186,187,190,191,193 85% prokaryotic sequences. (Descriptions of some sequences were 195,197,202,213,215,217,220 not readily available.) The file containing the sequence descriptions 221,223,224,226,235,241,243 can be found in the attachment, under the name 1gw9A.descr. 245,246,247,249,253,254,255 257,260,261,282,283,285,286 287,289,298,300,303,306,307 2.3 Residue ranking in 1gw9A 308,311,313,317 blue 7 22,24,25,26,27,30,292 The 1gw9A sequence is shown in Figs. 1–2, with each residue colo- red according to its estimated importance. The full listing of residues continued in next column in 1gw9A can be found in the file called 1gw9A.ranks sorted in the attachment. 2 Fig. 4. Residues in 1gw9A, colored according to the cluster they belong to: 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 1. continued cluster size member color residues yellow 5 124,168,172,173,174 Table 1. Clusters of top ranking residues in 1gw9A. 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. Iodide ion binding site. Table 2 lists the top 25% of residues at the interface with 1gw9AIOD1400 (iodide ion). The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. res type subst’s cvg noc/ dist antn (%) bb (A˚ ) 137 W W(100) 0.09 1/1 4.83 site 141 E E(100) 0.09 3/0 4.13 138 G G(92) 0.18 2/2 3.71 P(7) Table 2. The top 25% of residues in 1gw9A at the interface with iodide ion.(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: distance of closest apporach to the ligand. ) 3 Table 3. type in the bracket; noc/bb: number of contacts with the ligand, with the num- res type disruptive ber of contacts realized through backbone atoms given in the bracket; dist: mutations distance of closest apporach to the ligand. ) 137 W (KE)(TQD)(SNCRG)(M) 141 E (FWH)(YVCARG)(T)(SNKLPI) 138 G (R)(KE)(H)(FYQWD) Table 5. res type disruptive Table 3. List of disruptive mutations for the top 25% of residues in mutations 1gw9A, that are at the interface with iodide ion. 16 W (KE)(TQD)(SNCRG)(M) 54 H (E)(TQMD)(SNKVCLAPIG)(YR) 94 F (E)(K)(TQD)(SNCG) Table 5. List of disruptive mutations for the top 25% of residues in 1gw9A, that are at the interface with iodide ion. Fig. 5. Residues in 1gw9A, at the interface with iodide ion, colored by their relative importance. The ligand (iodide ion) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, as well as on the line of sight to the ligand were removed. (See Appendix for the coloring scheme for the protein chain 1gw9A.) Fig. 6. Residues in 1gw9A, at the interface with iodide ion, colored by their relative importance. The ligand (iodide ion) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, as well as on the line Figure 5 shows residues in 1gw9A colored by their importance, at the of sight to the ligand were removed. (See Appendix for the coloring scheme interface with 1gw9AIOD1400. for the protein chain 1gw9A.) Iodide ion binding site. Table 4 lists the top 25% of residues at the interface with 1gw9AIOD1410 (iodide ion). The following table (Table 5) suggests possible disruptive replacements for these residues Figure 6 shows residues in 1gw9A colored by their importance, at the (see Section 3.6). interface with 1gw9AIOD1410. Iodide ion binding site. Table 6 lists the top 25% of residues at Table 4. the interface with 1gw9AIOD1405 (iodide ion). The following table res type subst’s cvg noc/ dist antn (Table 7) suggests possible disruptive replacements for these residues (%) bb (A˚ ) (see Section 3.6). 16 W W(100) 0.09 4/0 4.04 Table 6. 54 H H(100) 0.09 3/0 4.34 site res type subst’s cvg noc/ dist 94 F F(96) 0.15 2/0 3.88 (%) bb (A˚ ) H(3) 24 D D(100) 0.09 5/1 3.72 25 P P(88) 0.21 4/1 3.02 Table 4. The top 25% of residues in 1gw9A at the interface with iodide continued in next column ion.(Field names: res: residue number in the PDB entry; type: amino acid type; substs: substitutions seen in the alignment; with the percentage of each 4 Table 6. continued Beta-l-xylopyranose binding site. Table 8 lists the top res type subst’s cvg noc/ dist 25% of residues at the interface with 1gw9ALXC1390 (beta-l- (%) bb (A˚ ) xylopyranose). The following table (Table 9) suggests possible Q(11) disruptive replacements for these residues (see Section 3.6).