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2D3p Lichtarge Lab 2006 Pages 1–8 2d3p Evolutionary trace report by report maker June 6, 2010 4.3.1 Alistat 7 4.3.2 CE 7 4.3.3 DSSP 7 4.3.4 HSSP 8 4.3.5 LaTex 8 4.3.6 Muscle 8 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 2d3p): Title: Cratylia floribunda seed lectin crystallized at basic ph Compound: Mol id: 1; molecule: lectin alpha chain; chain: a, b, c, d Organism, scientific name: Cratylia Floribunda; 2d3p contains a single unique chain 2d3pA (236 residues long) and its homologues 2d3pD, 2d3pC, and 2d3pB. CONTENTS 2 CHAIN 2D3PA 2.1 P81517 overview 1 Introduction 1 From SwissProt, id P81517, 99% identical to 2d3pA: 2 Chain 2d3pA 1 Description: Lectin alpha chain [Contains: Lectin beta chain; Lectin 2.1 P81517 overview 1 gamma chain]. 2.2 Multiple sequence alignment for 2d3pA 1 Organism, scientific name: Cratylia floribunda. 2.3 Residue ranking in 2d3pA 1 Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; 2.4 Top ranking residues in 2d3pA 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; Cratylia. 2.4.2 Overlap with known functional surfaces at Function: D-mannose/D-glucose-binding lectin. Mixture of 60lectin 25% coverage. 2 and 40 2.4.3 Possible novel functional surfaces at 25% Subunit: pH-dependent homodimer of alpha chains at pH values coverage. 5 lower than 6.5 and a homotetramer of alpha chains above this value. Tissue specificity: Seed. 3 Notes on using trace results 6 Ptm: The beta and gamma chains are produced by partial proteolytic 3.1 Coverage 6 processing of the lectin alpha chain by an asparaginyl endopeptidase. 3.2 Known substitutions 6 Mass spectrometry: MW=25397; MW ERR=3; 3.3 Surface 6 METHOD=Electrospray; RANGE=1-236; NOTE=Ref.2. 3.4 Number of contacts 7 Mass spectrometry: MW=12847; MW ERR=2; 3.5 Annotation 7 METHOD=Electrospray; RANGE=1-118; NOTE=Ref.2. 3.6 Mutation suggestions 7 Mass spectrometry: MW=12568; MW ERR=2; METHOD=Electrospray; RANGE=119-236; NOTE=Ref.2. 4 Appendix 7 Miscellaneous: Binds one manganese (or other transition metal) ion 4.1 File formats 7 and one calcium ion. The metal ions are essential for the saccharide- 4.2 Color schemes used 7 binding and cell-agglutinating activities. 4.3 Credits 7 Similarity: Belongs to the leguminous lectin family. 1 Lichtarge lab 2006 in 2d3pA can be found in the file called 2d3pA.ranks sorted in the attachment. 2.4 Top ranking residues in 2d3pA 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 2d3pA colored by their importance: bright red and yellow indicate more conser- Fig. 1. Residues 1-118 in 2d3pA colored by their relative importance. (See ved/important residues (see Appendix for the coloring scheme). A Appendix, Fig.9, for the coloring scheme.) Pymol script for producing this figure can be found in the attachment. Fig. 2. Residues 119-236 in 2d3pA colored by their relative importance. (See Appendix, Fig.9, for the coloring scheme.) About: This Swiss-Prot entry is copyright. It is produced through a collaboration between the Swiss Institute of Bioinformatics and the EMBL outstation - the European Bioinformatics Institute. There are no restrictions on its use as long as its content is in no way modified and this statement is not removed. 2.2 Multiple sequence alignment for 2d3pA For the chain 2d3pA, the alignment 2d3pA.msf (attached) with 26 sequences was used. The alignment was downloaded from the HSSP database, and fragments shorter than 75% of the query as well as duplicate sequences were removed. It can be found in the attachment to this report, under the name of 2d3pA.msf. Its statistics, from the Fig. 3. Residues in 2d3pA, colored by their relative importance. Clockwise: alistat program are the following: front, back, top and bottom views. Format: MSF Number of sequences: 26 Total number of residues: 5760 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the Smallest: 188 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: 221.5 in Table 1. Alignment length: 236 Average identity: 36% Table 1. Most related pair: 99% cluster size member Most unrelated pair: 19% color residues Most distant seq: 31% red 51 5,6,7,8,9,10,14,19,20,24,26 27,28,29,31,34,37,52,54,56 60,61,62,63,75,76,77,79,80 Furthermore, 2% of residues show as conserved in this alignment. 81,85,86,87,89,92,93,94,95 The alignment consists of 34% eukaryotic ( 34% plantae) 97,98,102,104,106,108,109 sequences. (Descriptions of some sequences were not readily availa- 111,113,171,178,220,231 ble.) The file containing the sequence descriptions can be found in blue 3 48,49,50 the attachment, under the name 2d3pA.descr. yellow 2 223,233 2.3 Residue ranking in 2d3pA Table 1. Clusters of top ranking residues in 2d3pA. The 2d3pA sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues 2 Fig. 4. Residues in 2d3pA, 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. 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. Calcium ion binding site. Table 2 lists the top 25% of residues at the interface with 2d3pCA237 (calcium 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) 0.03 4/0 2.41 24 H H(100) 0.03 1/0 4.74 14 N N(92) 0.07 6/2 2.37 D(7) 19 D D(80) 0.15 4/0 2.38 E(7) N(7) Y(3) 12 Y F(7) 0.25 5/4 2.39 Y(76) R(7) H(7) Table 2. The top 25% of residues in 2d3pA 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. ) 3 Table 3. Table 4. continued res type disruptive res type subst’s cvg noc/ dist mutations (%) bb (A˚ ) 10 D (R)(FWH)(KYVCAG)(TQM) K(3) 24 H (E)(TQMD)(SNKVCLAPIG)(YR) 108 S S(84) 0.13 11/3 2.71 14 N (Y)(FWH)(TR)(VCAG) G(3) 19 D (R)(FWH)(VA)(KCG) N(3) 12 Y (K)(EQM)(NVLAPDI)(R) Y(7) 75 V L(57) 0.14 1/1 4.80 Table 3. List of disruptive mutations for the top 25% of residues in V(38) 2d3pA, that are at the interface with calcium ion. Y(3) 62 S S(76) 0.16 19/2 3.84 .(7) T(7) K(3) A(3) 63 A V(53) 0.18 4/4 4.11 A(42) M(3) 49 T H(26) 0.20 27/0 3.17 D(7) T(53) N(11) 76 S S(69) 0.24 1/0 4.99 Y(19) I(3) N(3) W(3) Table 4. The top 25% of residues in 2d3pA at the interface with 2d3pD. (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. ) Fig. 5. Residues in 2d3pA, at the interface with calcium ion, colored by their relative importance. The ligand (calcium ion) is colored green. Atoms further Table 5. 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 res type disruptive for the protein chain 2d3pA.) mutations 109 W (KE)(QD)(TR)(N) 60 R (T)(Y)(D)(SCG) Figure 5 shows residues in 2d3pA colored by their importance, at the 108 S (KR)(M)(FQWH)(E) interface with 2d3pCA237. 75 V (K)(R)(E)(YQ) Interface with 2d3pD.Table 4 lists the top 25% of residues at the 62 S (R)(K)(FWH)(QM) interface with 2d3pD. The following table (Table 5) suggests possible 63 A (Y)(R)(KE)(H) disruptive replacements for these residues (see Section 3.6). 49 T (R)(K)(FMW)(QH) 76 S (KR)(Q)(EMH)(FW) Table 4. res type subst’s cvg noc/ dist (%) bb (A˚ ) Table 5.
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