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Pages 1–9 1n47 Evolutionary trace report by report maker June 16, 2009 4.3.1 Alistat 8 4.3.2 CE 9 4.3.3 DSSP 9 4.3.4 HSSP 9 4.3.5 LaTex 9 4.3.6 Muscle 9 4.3.7 Pymol 9 4.4 Note about ET Viewer 9 4.5 Citing this work 9 4.6 About report maker 9 4.7 Attachments 9 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1n47): Title: Isolectin b4 from vicia villosa in complex with the tn antigen Compound: Mol id: 1; molecule: isolectin b4; chain: a, b, c, d CONTENTS Organism, scientific name: Vicia Villosa; 1n47 contains a single unique chain 1n47A (233 residues long) and 1 Introduction 1 its homologues 1n47D, 1n47C, and 1n47B. 2 Chain 1n47A 1 2.1 Q9ZWP5 overview 1 2.2 Multiple sequence alignment for 1n47A 1 2.3 Residue ranking in 1n47A 1 2.4 Top ranking residues in 1n47A and their position on 2 CHAIN 1N47A the structure 2 2.1 Q9ZWP5 overview 2.4.1 Clustering of residues at 25% coverage. 2 2.4.2 Overlap with known functional surfaces at From SwissProt, id Q9ZWP5, 54% identical to 1n47A: 25% coverage. 2 Description: Lectin. 2.4.3 Possible novel functional surfaces at 25% Organism, scientific name: Robinia pseudoacacia (Black locust). coverage. 5 Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core 3 Notes on using trace results 7 eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoi- 3.1 Coverage 7 deae; Robinieae; Robinia. 3.2 Known substitutions 7 3.3 Surface 8 3.4 Number of contacts 8 3.5 Annotation 8 2.2 Multiple sequence alignment for 1n47A 3.6 Mutation suggestions 8 For the chain 1n47A, the alignment 1n47A.msf (attached) with 331 sequences was used. The alignment was downloaded from the HSSP 4 Appendix 8 database, and fragments shorter than 75% of the query as well as 4.1 File formats 8 duplicate sequences were removed. It can be found in the attachment 4.2 Color schemes used 8 to this report, under the name of 1n47A.msf. Its statistics, from the 4.3 Credits 8 alistat program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 1-116 in 1n47A colored by their relative importance. (See Appendix, Fig.11, for the coloring scheme.) Fig. 2. Residues 117-233 in 1n47A colored by their relative importance. (See Appendix, Fig.11, for the coloring scheme.) Fig. 3. Residues in 1n47A, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 331 Total number of residues: 73572 Smallest: 175 belong to. The clusters in Fig.4 are composed of the residues listed Largest: 233 Average length: 222.3 Alignment length: 233 Average identity: 37% Most related pair: 99% Most unrelated pair: 12% Most distant seq: 33% Furthermore, <1% of residues show as conserved in this ali- gnment. The alignment consists of 60% eukaryotic ( 60% plantae), and <1% prokaryotic sequences. (Descriptions of some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 1n47A.descr. 2.3 Residue ranking in 1n47A The 1n47A sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues in 1n47A can be found in the file called 1n47A.ranks sorted in the attachment. 2.4 Top ranking residues in 1n47A and their position on the structure In the following we consider residues ranking among top 25% of Fig. 4. Residues in 1n47A, colored according to the cluster they belong to: residues in the protein . Figure 3 shows residues in 1n47A colored red, followed by blue and yellow are the largest clusters (see Appendix for by their importance: bright red and yellow indicate more conser- the coloring scheme). Clockwise: front, back, top and bottom views. The ved/important residues (see Appendix for the coloring scheme). A corresponding Pymol script is attached. Pymol script for producing this figure can be found in the attachment. in Table 1. 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 2 Table 1. cluster size member color residues red 54 6,11,32,34,35,48,49,50,51,52 65,66,67,69,71,84,85,86,89 90,91,105,106,107,108,120 121,122,123,124,125,126,129 132,137,138,139,140,141,143 147,165,167,174,195,206,207 208,211,212,226,227,228,232 blue 2 55,203 Table 1. Clusters of top ranking residues in 1n47A. 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 1n47B.Table 2 lists the top 25% of residues at the interface with 1n47B. The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. Fig. 5. Residues in 1n47A, at the interface with 1n47B, colored by their rela- res type subst’s cvg noc/ dist tive importance. 1n47B is shown in backbone representation (See Appendix (%) bb (A˚ ) for the coloring scheme for the protein chain 1n47A.) 55 P P(86) 0.14 25/7 3.57 R(1) Q(4)K Figure 5 shows residues in 1n47A colored by their importance, at the A(3) interface with 1n47B. L(1)TYG Manganese (ii) ion binding site. Table 4 lists the top 25% of resi- S. dues at the interface with 1n47AMN253 (manganese (ii) ion). The 6 F F(90)ST 0.15 13/9 3.37 following table (Table 5) suggests possible disruptive replacements L(1) for these residues (see Section 3.6). I(1) Table 4. .(2)DA res type subst’s cvg noc/ dist Y(1)VW (%) bb (A˚ ) 52 Y Y(82) 0.18 10/0 3.67 125 D D(92) 0.03 4/0 1.93 H(8) N(3)VGF F(6)CLS L(1)TIK AWG. 123 E E(87) 0.04 4/0 2.32 Table 2. The top 25% of residues in 1n47A at the interface with 1n47B. V(7) (Field names: res: residue number in the PDB entry; type: amino acid type; A(3)DWC substs: substitutions seen in the alignment; with the percentage of each type KQ. 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 137 H H(84) 0.04 5/0 2.49 of closest apporach to the ligand. ) R(4) S(3) .(1)LAE Table 3. D(1) res type disruptive Q(1)IPG mutations 147 S S(88) 0.06 1/0 4.29 55 P (Y)(R)(H)(T) P(7)DHW 6 F (K)(E)(Q)(R) IV.KNEF 52 Y (K)(Q)(E)(M) A 132 D D(81) 0.07 5/1 2.39 Table 3. List of disruptive mutations for the top 25% of residues in continued in next column 1n47A, that are at the interface with 1n47B. 3 Table 4. continued Figure 6 shows residues in 1n47A colored by their importance, at the res type subst’s cvg noc/ dist interface with 1n47AMN253. (%) bb (A˚ ) Calcium ion binding site. Table 6 lists the top 25% of residues at .(9) the interface with 1n47ACA252 (calcium ion). The following table E(4) (Table 7) suggests possible disruptive replacements for these residues S(2)YNH (see Section 3.6). LKR Table 6. res type subst’s cvg noc/ dist Table 4. The top 25% of residues in 1n47A at the interface with manga- A˚ nese (ii) ion.(Field names: res: residue number in the PDB entry; type: amino (%) bb ( ) acid type; substs: substitutions seen in the alignment; with the percentage of 125 D D(92) 0.03 4/0 2.43 each type in the bracket; noc/bb: number of contacts with the ligand, with N(3)VGF the number of contacts realized through backbone atoms given in the bracket; L(1)TIK dist: distance of closest apporach to the ligand. ) . 137 H H(84) 0.04 1/0 4.78 R(4) S(3) Table 5. .(1)LAE res type disruptive D(1) mutations Q(1)IPG 125 D (R)(H)(FW)(Y) 132 D D(81) 0.07 4/0 2.25 123 E (H)(FW)(Y)(R) .(9) 137 H (E)(T)(QD)(M) E(4) 147 S (R)(K)(H)(Q) S(2)YNH 132 D (R)(FW)(H)(YVCAG) LKR 85 D D(59) 0.16 2/1 4.63 Y(10) Table 5. List of disruptive mutations for the top 25% of residues in 1n47A, that are at the interface with manganese (ii) ion. H(12) E(4) V(2)S N(1)T A(1)P F(2) G(2)IR. Q 129 N N(73) 0.20 6/2 2.71 A(2) D(8) S(7) G(2)R Y(3) Q(1)KET H Table 6. The top 25% of residues in 1n47A at the interface with calcium 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.

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