2Eig Lichtarge Lab 2006

Pages 1–8 2eig Evolutionary trace report by report maker September 6, 2008 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 7 4.4 Note about ET Viewer 7 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 2eig): Title: Lotus tetragonolobus seed lectin (isoform) Compound: Mol id: 1; molecule: lectin; chain: a, b, c, d Organism, scientific name: Lotus Tetragonolobus; 2eig contains a single unique chain 2eigA (230 residues long) and its homologues 2eigD, 2eigC, and 2eigB. CONTENTS 2 CHAIN 2EIGA 1 Introduction 1 2.1 P19664 overview 2 Chain 2eigA 1 From SwissProt, id P19664, 81% identical to 2eigA: 2.1 P19664 overview 1 Description: Anti-H(O) lectin (LTA). 2.2 Multiple sequence alignment for 2eigA 1 Organism, scientific name: Lotus tetragonolobus (Winged pea) 2.3 Residue ranking in 2eigA 1 (Tetragonolobus purpureus). 2.4 Top ranking residues in 2eigA and their position on Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; the structure 1 Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core 2.4.1 Clustering of residues at 25% coverage. 2 eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoi- 2.4.2 Overlap with known functional surfaces at deae; Loteae; Lotus. 25% coverage. 2 Function: L-fucose specific lectin. 2.4.3 Possible novel functional surfaces at 25% Similarity: Belongs to the leguminous lectin family. coverage. 4 About: This Swiss-Prot entry is copyright. It is produced through a collaboration between the Swiss Institute of Bioinformatics and the 3 Notes on using trace results 6 EMBL outstation - the European Bioinformatics Institute. There are 3.1 Coverage 6 no restrictions on its use as long as its content is in no way modified 3.2 Known substitutions 6 and this statement is not removed. 3.3 Surface 6 3.4 Number of contacts 6 2.2 Multiple sequence alignment for 2eigA 3.5 Annotation 6 3.6 Mutation suggestions 6 For the chain 2eigA, the alignment 2eigA.msf (attached) with 61 sequences was used. The alignment was assembled through combi- 4 Appendix 7 nation of BLAST searching on the UniProt database and alignment 4.1 File formats 7 using Muscle program. It can be found in the attachment to this 4.2 Color schemes used 7 report, under the name of 2eigA.msf. Its statistics, from the alistat 4.3 Credits 7 program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 1-115 in 2eigA colored by their relative importance. (See Appendix, Fig.11, for the coloring scheme.) Fig. 2. Residues 116-230 in 2eigA colored by their relative importance. (See Appendix, Fig.11, for the coloring scheme.) Fig. 3. Residues in 2eigA, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 61 Total number of residues: 13061 Smallest: 191 Largest: 230 Average length: 214.1 Alignment length: 230 Average identity: 46% Most related pair: 99% Most unrelated pair: 23% Most distant seq: 40% Furthermore, 1% of residues show as conserved in this alignment. The alignment consists of 98% eukaryotic ( 98% 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 2eigA.descr. 2.3 Residue ranking in 2eigA The 2eigA sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues in 2eigA can be found in the file called 2eigA.ranks sorted in the attachment. 2.4 Top ranking residues in 2eigA and their position on Fig. 4. Residues in 2eigA, colored according to the cluster they belong to: the structure red, followed by blue and yellow are the largest clusters (see Appendix for the coloring scheme). Clockwise: front, back, top and bottom views. The In the following we consider residues ranking among top 25% of resi- corresponding Pymol script is attached. dues in the protein . Figure 3 shows residues in 2eigA colored by their importance: bright red and yellow indicate more conserved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the top 25% of all residues, this time colored according to clusters they belong to. The clusters in Fig.4 are composed of the residues listed in Table 1. 2 Table 1. cluster size member color residues red 54 3,8,17,28,30,41,42,43,44,45 48,51,59,60,61,62,64,66,68 81,83,84,86,94,102,103,104 105,115,117,118,119,121,138 139,145,161,163,164,165,172 192,200,202,203,204,205,206 207,214,221,222,223,225 Table 1. Clusters of top ranking residues in 2eigA. 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. NAG binding site. Table 2 lists the top 25% of residues at the interface with 2eigANAG1001 (nag). The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. Fig. 5. Residues in 2eigA, at the interface with NAG, colored by their relative res type subst’s cvg noc/ dist antn importance. The ligand (NAG) is colored green. Atoms further than 30A˚ away (%) bb (A˚ ) from the geometric center of the ligand, as well as on the line of sight to the 222 S S(98) 0.04 8/0 3.57 site ligand were removed. (See Appendix for the coloring scheme for the protein T(1) chain 2eigA.) Table 2. The top 25% of residues in 2eigA at the interface with Table 4. NAG.(Field names: res: residue number in the PDB entry; type: amino acid continued type; substs: substitutions seen in the alignment; with the percentage of each res type subst’s cvg noc/ dist antn type in the bracket; noc/bb: number of contacts with the ligand, with the num- (%) bb (A˚ ) ber of contacts realized through backbone atoms given in the bracket; dist: E(3) distance of closest apporach to the ligand. ) N(3) 145 S S(63) 0.20 1/0 4.19 P(27) Table 3. L(3) res type disruptive D(1) mutations .(1) 222 S (KR)(FQMWH)(NELPI)(Y) F(1) 118 E E(68) 0.22 4/0 2.19 site Table 3. List of disruptive mutations for the top 25% of residues in 2eigA, V(18) that are at the interface with NAG. A(9) C(1) Figure 5 shows residues in 2eigA colored by their importance, at the F(1) interface with 2eigANAG1001. Manganese (ii) ion binding site. Table 4 lists the top 25% of resi- Table 4. The top 25% of residues in 2eigA at the interface with manga- dues at the interface with 2eigAMN1101 (manganese (ii) ion). The nese (ii) ion.(Field names: res: residue number in the PDB entry; type: amino following table (Table 5) suggests possible disruptive replacements acid type; substs: substitutions seen in the alignment; with the percentage of for these residues (see Section 3.6). 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; Table 4. dist: distance of closest apporach to the ligand. ) res type subst’s cvg noc/ dist antn (%) bb (A˚ ) 127 D D(63) 0.19 5/1 2.15 site Table 5. .(19) res type disruptive S(9) mutations continued in next column continued in next column 3 Table 5. continued 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. ) 127 D (R)(FWH)(Y)(VCAG) 145 S (R)(K)(H)(Q) 118 E (HR)(Y)(FW)(K) Table 7. res type disruptive mutations Table 5. List of disruptive mutations for the top 25% of residues in 2eigA, that are at the interface with manganese (ii) ion. 127 D (R)(FWH)(Y)(VCAG) Table 7. List of disruptive mutations for the top 25% of residues in 2eigA, that are at the interface with calcium ion. Fig. 6. Residues in 2eigA, at the interface with manganese (ii) ion, colored by their relative importance. The ligand (manganese (ii) 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 Fig. 7. Residues in 2eigA, at the interface with calcium ion, colored by their coloring scheme for the protein chain 2eigA.) relative importance. The ligand (calcium 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 Figure 6 shows residues in 2eigA colored by their importance, at the for the protein chain 2eigA.) interface with 2eigAMN1101. Calcium ion binding site. Table 6 lists the top 25% of residues at the interface with 2eigACA1102 (calcium ion). The following table Figure 7 shows residues in 2eigA colored by their importance, at the (Table 7) suggests possible disruptive replacements for these residues interface with 2eigACA1102.

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