Pages 1–8 1wuv Evolutionary trace report by report maker April 13, 2009 4.3.1 Alistat 7 4.3.2 CE 7 4.3.3 DSSP 7 4.3.4 HSSP 7 4.3.5 LaTex 7 4.3.6 Muscle 7 4.3.7 Pymol 8 4.4 Note about ET Viewer 8 4.5 Citing this work 8 4.6 About report maker 8 4.7 Attachments 8 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1wuv): Title: Crystal structure of native canavalia gladiata lectin (cgl) : a tetrameric cona-like lectin Compound: Mol id: 1; molecule: concanavalin a; chain: a, d, g, j; synonym: lectin Organism, scientific name: Canavalia Gladiata; 1wuv contains a single unique chain 1wuvA (237 residues long) and its homologues 1wuvJ, 1wuvD, and 1wuvG. CONTENTS 2 CHAIN 1WUVA 1 Introduction 1 2.1 P81461 overview 2 Chain 1wuvA 1 From SwissProt, id P81461, 99% identical to 1wuvA: 2.1 P81461 overview 1 Description: Concanavalin A (Con A). 2.2 Multiple sequence alignment for 1wuvA 1 Organism, scientific name: Canavalia virosa. 2.3 Residue ranking in 1wuvA 1 Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; 2.4 Top ranking residues in 1wuvA and their position on Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core the structure 2 eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoi- 2.4.1 Clustering of residues at 25% coverage. 2 deae; Phaseoleae; Canavalia. 2.4.2 Overlap with known functional surfaces at Function: Glucose/D-mannose specific lectin. 25% coverage. 2 Subunit: Homotetramer. 2.4.3 Possible novel functional surfaces at 25% Miscellaneous: Binds one manganese (or other transition metal) ion coverage. 5 and one calcium ion. The metal ions are essential for the saccharide- binding and cell-agglutinating activities. 3 Notes on using trace results 6 Similarity: Belongs to the leguminous lectin family. 3.1 Coverage 6 About: This Swiss-Prot entry is copyright. It is produced through a 3.2 Known substitutions 6 collaboration between the Swiss Institute of Bioinformatics and the 3.3 Surface 6 EMBL outstation - the European Bioinformatics Institute. There are 3.4 Number of contacts 6 no restrictions on its use as long as its content is in no way modified 3.5 Annotation 6 and this statement is not removed. 3.6 Mutation suggestions 6 2.2 Multiple sequence alignment for 1wuvA 4 Appendix 7 For the chain 1wuvA, the alignment 1wuvA.msf (attached) with 25 4.1 File formats 7 sequences was used. The alignment was downloaded from the HSSP 4.2 Color schemes used 7 database, and fragments shorter than 75% of the query as well as 4.3 Credits 7 duplicate sequences were removed. It can be found in the attachment 1 Lichtarge lab 2006 Fig. 1. Residues 1-118 in 1wuvA colored by their relative importance. (See Appendix, Fig.10, for the coloring scheme.) Fig. 2. Residues 119-237 in 1wuvA colored by their relative importance. (See Appendix, Fig.10, for the coloring scheme.) Fig. 3. Residues in 1wuvA, colored by their relative importance. Clockwise: front, back, top and bottom views. to this report, under the name of 1wuvA.msf. Its statistics, from the alistat program are the following: 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Format: MSF top 25% of all residues, this time colored according to clusters they Number of sequences: 25 belong to. The clusters in Fig.4 are composed of the residues listed Total number of residues: 5516 Smallest: 182 Largest: 237 Average length: 220.6 Alignment length: 237 Average identity: 39% Most related pair: 98% Most unrelated pair: 19% Most distant seq: 30% Furthermore, 3% of residues show as conserved in this alignment. The alignment consists of 36% eukaryotic ( 36% plantae) sequences. (Descriptions of some sequences were not readily availa- ble.) The file containing the sequence descriptions can be found in the attachment, under the name 1wuvA.descr. 2.3 Residue ranking in 1wuvA The 1wuvA sequence is shown in Figs. 1–2, with each residue colo- red according to its estimated importance. The full listing of residues in 1wuvA can be found in the file called 1wuvA.ranks sorted in the attachment. 2.4 Top ranking residues in 1wuvA and their position on the structure In the following we consider residues ranking among top 25% of Fig. 4. Residues in 1wuvA, colored according to the cluster they belong to: red, followed by blue and yellow are the largest clusters (see Appendix for residues in the protein . Figure 3 shows residues in 1wuvA colored the coloring scheme). Clockwise: front, back, top and bottom views. The by their importance: bright red and yellow indicate more conser- corresponding Pymol script is attached. ved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. in Table 1. 2 Table 1. cluster size member color residues red 46 4,5,6,7,8,9,10,14,19,20,24 26,27,28,29,30,31,34,37,40 45,46,48,49,50,51,52,54,55 56,60,61,62,63,64,74,75,76 77,79,80,81,85,86,87,89 blue 11 92,93,94,95,97,98,102,104 106,108,109 yellow 3 111,113,114 Table 1. Clusters of top ranking residues in 1wuvA. 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. Manganese (ii) ion binding site. Table 2 lists the top 25% of resi- dues at the interface with 1wuvAMN239 (manganese (ii) 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 (%) bb (A˚ ) 10 D D(100) 0.04 4/0 2.14 24 H H(100) 0.04 5/0 2.13 19 D D(95) 0.08 5/1 2.26 N(4) 8 E E(95) 0.09 4/0 2.18 T(4) 34 S S(95) 0.10 1/0 4.12 X(4) Table 2. The top 25% of residues in 1wuvA at the interface with manga- nese (ii) 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 number of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) Table 3. res type disruptive mutations 10 D (R)(FWH)(KYVCAG)(TQM) 24 H (E)(TQMD)(SNKVCLAPIG)(YR) 19 D (R)(FWH)(Y)(VCAG) 8 E (FWH)(R)(YVA)(KCG) 34 S (KR)(FQMWH)(YE)(NLPI) Table 3. List of disruptive mutations for the top 25% of residues in 1wuvA, that are at the interface with manganese (ii) ion. Figure 5 shows residues in 1wuvA colored by their importance, at the interface with 1wuvAMN239. Interface with 1wuvG1.By analogy with 1wuvG – 1wuvG1 inter- face. Table 4 lists the top 25% of residues at the interface with 3 Table 4. continued res type subst’s cvg noc/ dist (%) bb (A˚ ) D(11) T(44) N(4) Q(4) 64 V V(76) 0.23 15/2 3.08 F(8) I(8) K(4) R(4) 51 H S(35) 0.24 23/0 3.54 W(20) H(35) I(4) V(4) 55 N T(28) 0.25 22/0 3.56 N(56) D(16) Table 4. The top 25% of residues in 1wuvA at the interface with 1wuvG1. Fig. 5. Residues in 1wuvA, at the interface with manganese (ii) ion, colored (Field names: res: residue number in the PDB entry; type: amino acid type; by their relative importance. The ligand (manganese (ii) ion) is colored green. substs: substitutions seen in the alignment; with the percentage of each type Atoms further than 30A˚ away from the geometric center of the ligand, as well in the bracket; noc/bb: number of contacts with the ligand, with the number of as on the line of sight to the ligand were removed. (See Appendix for the contacts realized through backbone atoms given in the bracket; dist: distance coloring scheme for the protein chain 1wuvA.) of closest apporach to the ligand. ) 1wuvG1. The following table (Table 5) suggests possible disruptive Table 5. replacements for these residues (see Section 3.6). res type disruptive mutations Table 4. 108 S (KR)(FQMWH)(E)(NYLPI) res type subst’s cvg noc/ dist 75 V (YR)(KE)(H)(QD) (%) bb (A˚ ) 76 S (K)(R)(QM)(FNELWPHI) 108 S S(95) 0.04 5/0 3.97 60 R (T)(Y)(D)(SECG) G(4) 62 S (R)(K)(H)(FQW) 75 V L(64) 0.12 1/1 4.76 63 A (Y)(R)(KE)(H) V(35) 74 T (R)(K)(H)(FW) 76 S S(83) 0.13 8/0 3.48 49 T (R)(FKW)(H)(M) Y(16) 64 V (Y)(E)(D)(KR) 60 R N(52) 0.14 48/0 2.36 51 H (E)(Q)(D)(K) R(40) 55 N (Y)(FWH)(R)(TVA) I(8) 62 S S(88) 0.16 20/3 3.23 T(4) Table 5. List of disruptive mutations for the top 25% of residues in D(4) 1wuvA, that are at the interface with 1wuvG1. A(4) 63 A V(56) 0.18 4/4 3.63 Figure 6 shows residues in 1wuvA colored by their importance, at the A(40) interface with 1wuvG1.