Pages 1–9 1mvq Evolutionary trace report by report maker May 9, 2010 4.3.1 Alistat 8 4.3.2 CE 8 4.3.3 DSSP 8 4.3.4 HSSP 8 4.3.5 LaTex 8 4.3.6 Muscle 8 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 1mvq): Title: Cratylia mollis lectin (isoform 1) in complex with methyl- alpha-d-mannose Compound: Mol id: 1; molecule: lectin, isoform 1; chain: a Organism, scientific name: Cratylia Mollis; 1mvq contains a single unique chain 1mvqA (236 residues long). 2 CHAIN 1MVQA CONTENTS 2.1 P83721 overview 1 Introduction 1 From SwissProt, id P83721, 99% identical to 1mvqA: Description: Mannose/glucose-specific lectin Cramoll (Iso1) [Con- 2 Chain 1mvqA 1 tains: Cramoll alpha chain; Cramoll beta chain] (Fragments). 2.1 P83721 overview 1 Organism, scientific name: Cratylia mollis (Camaratu bean). 2.2 Multiple sequence alignment for 1mvqA 1 Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; 2.3 Residue ranking in 1mvqA 1 Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core 2.4 Top ranking residues in 1mvqA and their position on eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoi- the structure 2 deae; Phaseoleae; Cratylia. 2.4.1 Clustering of residues at 25% coverage. 2 Function: Glucose/D-mannose specific lectin. 2.4.2 Overlap with known functional surfaces at Subunit: Homotetramer. 25% coverage. 2 Ptm: The alpha and beta chains are produced by partial proteolytic 2.4.3 Possible novel functional surfaces at 25% processing of the lectin precursor by an asparaginyl endopeptidase. coverage. 5 Miscellaneous: Binds one manganese (or other transition metal) ion and one calcium ion. The metal ions are essential for the saccharide- 3 Notes on using trace results 7 binding and cell-agglutinating activities. 3.1 Coverage 7 Similarity: Belongs to the leguminous lectin family. 3.2 Known substitutions 7 About: This Swiss-Prot entry is copyright. It is produced through a 3.3 Surface 7 collaboration between the Swiss Institute of Bioinformatics and the 3.4 Number of contacts 7 EMBL outstation - the European Bioinformatics Institute. There are 3.5 Annotation 7 no restrictions on its use as long as its content is in no way modified 3.6 Mutation suggestions 8 and this statement is not removed. 4 Appendix 8 2.2 Multiple sequence alignment for 1mvqA 4.1 File formats 8 For the chain 1mvqA, the alignment 1mvqA.msf (attached) with 23 4.2 Color schemes used 8 sequences was used. The alignment was downloaded from the HSSP 4.3 Credits 8 database, and fragments shorter than 75% of the query as well as 1 Lichtarge lab 2006 Pymol script for producing this figure can be found in the attachment. Fig. 1. Residues 1-118 in 1mvqA colored by their relative importance. (See Appendix, Fig.12, for the coloring scheme.) Fig. 2. Residues 119-236 in 1mvqA colored by their relative importance. (See Appendix, Fig.12, for the coloring scheme.) duplicate sequences were removed. It can be found in the attachment to this report, under the name of 1mvqA.msf. Its statistics, from the alistat program are the following: Fig. 3. Residues in 1mvqA, colored by their relative importance. Clockwise: front, back, top and bottom views. Format: MSF Number of sequences: 23 Total number of residues: 5108 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Smallest: 194 top 25% of all residues, this time colored according to clusters they Largest: 236 belong to. The clusters in Fig.4 are composed of the residues listed Average length: 222.1 in Table 1. Alignment length: 236 Table 1. Average identity: 37% cluster size member Most related pair: 99% color residues Most unrelated pair: 18% red 49 6,7,8,9,10,11,14,19,20,24,26 Most distant seq: 31% 27,34,40,52,54,56,60,61,62 63,75,76,77,79,80,81,85,86 87,89,92,93,94,95,97,98,102 Furthermore, 2% of residues show as conserved in this alignment. 104,108,109,111,113,165,171 The alignment consists of 39% eukaryotic ( 39% plantae) 172,178,190,229 sequences. (Descriptions of some sequences were not readily availa- blue 3 29,30,31 ble.) The file containing the sequence descriptions can be found in yellow 2 159,162 the attachment, under the name 1mvqA.descr. green 2 49,50 2.3 Residue ranking in 1mvqA Table 1. The 1mvqA sequence is shown in Figs. 1–2, with each residue colo- Clusters of top ranking residues in 1mvqA. red according to its estimated importance. The full listing of residues in 1mvqA can be found in the file called 1mvqA.ranks sorted in the 2.4.2 Overlap with known functional surfaces at 25% coverage. attachment. The name of the ligand is composed of the source PDB identifier 2.4 Top ranking residues in 1mvqA and their position and the heteroatom name used in that file. Calcium ion binding site. Table 2 lists the top 25% of residues at on the structure the interface with 1mvqACA237 (calcium ion). The following table In the following we consider residues ranking among top 25% of (Table 3) suggests possible disruptive replacements for these residues residues in the protein . Figure 3 shows residues in 1mvqA colored (see Section 3.6). by their importance: bright red and yellow indicate more conser- ved/important residues (see Appendix for the coloring scheme). A 2 Fig. 4. Residues in 1mvqA, colored according to the cluster they belong to: Fig. 5. Residues in 1mvqA, at the interface with calcium ion, colored by their red, followed by blue and yellow are the largest clusters (see Appendix for relative importance. The ligand (calcium ion) is colored green. Atoms further the coloring scheme). Clockwise: front, back, top and bottom views. The than 30A˚ away from the geometric center of the ligand, as well as on the line corresponding Pymol script is attached. of sight to the ligand were removed. (See Appendix for the coloring scheme for the protein chain 1mvqA.) Table 2. res type subst’s cvg noc/ dist Figure 5 shows residues in 1mvqA colored by their importance, at (%) bb (A˚ ) the interface with 1mvqACA237. 10 D D(100) 0.03 4/0 2.42 Interface with 1mvqA2.Table 4 lists the top 25% of residues at 24 H H(100) 0.03 2/0 4.64 the interface with 1mvqA2. The following table (Table 5) suggests 14 N N(95) 0.05 6/2 2.39 possible disruptive replacements for these residues (see Section 3.6). D(4) 19 D D(86) 0.14 4/0 2.40 Table 4. N(4) res type subst’s cvg noc/ dist Y(4) (%) bb (A˚ ) K(4) 87 E E(82) 0.11 1/0 4.69 A(4) Table 2. The top 25% of residues in 1mvqA at the interface with calcium D(13) 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 Table 4. The top 25% of residues in 1mvqA at the interface with type in the bracket; noc/bb: number of contacts with the ligand, with the num- 1mvqA2. (Field names: res: residue number in the PDB entry; type: amino ber of contacts realized through backbone atoms given in the bracket; dist: acid type; substs: substitutions seen in the alignment; with the percentage of distance of closest apporach to the ligand. ) 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) Table 5. 24 H (E)(TQMD)(SNKVCLAPIG)(YR) res type disruptive 14 N (Y)(FWH)(TR)(VCAG) mutations 19 D (R)(FW)(H)(VA) 87 E (H)(FW)(R)(Y) Table 3. List of disruptive mutations for the top 25% of residues in Table 5. List of disruptive mutations for the top 25% of residues in 1mvqA, that are at the interface with calcium ion. 1mvqA, that are at the interface with 1mvqA2. 3 Table 7. res type disruptive mutations 14 N (Y)(FWH)(TR)(VCAG) 97 T (K)(FW)(MR)(H) 98 G (FWR)(H)(K)(E) Table 7. List of disruptive mutations for the top 25% of residues in 1mvqA, that are at the interface with o1-methyl-mannose. Fig. 6. Residues in 1mvqA, at the interface with 1mvqA2, colored by their relative importance. 1mvqA2 is shown in backbone representation (See Appendix for the coloring scheme for the protein chain 1mvqA.) Figure 6 shows residues in 1mvqA colored by their importance, at the interface with 1mvqA2. O1-methyl-mannose binding site. Table 6 lists the top 25% of residues at the interface with 1mvqMMA1 (o1-methyl-mannose). The following table (Table 7) suggests possible disruptive replace- ments for these residues (see Section 3.6). Table 6. res type subst’s cvg noc/ dist Fig. 7. Residues in 1mvqA, at the interface with o1-methyl-mannose, colo- (%) bb (A˚ ) red by their relative importance. The ligand (o1-methyl-mannose) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, 14 N N(95) 0.05 7/0 3.00 as well as on the line of sight to the ligand were removed. (See Appendix for D(4) the coloring scheme for the protein chain 1mvqA.) 97 T T(86) 0.10 1/1 4.52 S(4) R(8) Figure 7 shows residues in 1mvqA colored by their importance, at 98 G G(82) 0.16 17/17 3.27 the interface with 1mvqMMA1.