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1Cnv Lichtarge Lab 2006 Pages 1–6 1cnv Evolutionary trace report by report maker March 21, 2010 4.3.3 DSSP 5 4.3.4 HSSP 5 4.3.5 LaTex 5 4.3.6 Muscle 5 4.3.7 Pymol 5 4.4 Note about ET Viewer 5 4.5 Citing this work 5 4.6 About report maker 5 4.7 Attachments 6 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1cnv): Title: Crystal structure of concanavalin b at 1.65 a resolution Compound: Mol id: 1; molecule: concanavalin b; chain: a Organism, scientific name: Canavalia Ensiformis; 1cnv contains a single unique chain 1cnvA (283 residues long). CONTENTS 2 CHAIN 1CNVA 1 Introduction 1 2.1 P49347 overview 2 Chain 1cnvA 1 From SwissProt, id P49347, 95% identical to 1cnvA: 2.1 P49347 overview 1 Description: Concanavalin B precursor (Con B). 2.2 Multiple sequence alignment for 1cnvA 1 Organism, scientific name: Canavalia ensiformis (Jack bean) (Horse bean). 2.3 Residue ranking in 1cnvA 1 Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; 2.4 Top ranking residues in 1cnvA and their position on Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core the structure 1 eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoi- 2.4.1 Clustering of residues at 25% coverage. 2 deae; Phaseoleae; Canavalia. 2.4.2 Possible novel functional surfaces at 25% Function: May act as a carbohydrate-binding protein. coverage. 2 Similarity: Belongs to the glycosyl hydrolase 18 family. 3 Notes on using trace results 4 About: This Swiss-Prot entry is copyright. It is produced through a 3.1 Coverage 4 collaboration between the Swiss Institute of Bioinformatics and the 3.2 Known substitutions 4 EMBL outstation - the European Bioinformatics Institute. There are 3.3 Surface 4 no restrictions on its use as long as its content is in no way modified 3.4 Number of contacts 4 and this statement is not removed. 3.5 Annotation 4 3.6 Mutation suggestions 4 2.2 Multiple sequence alignment for 1cnvA 4 Appendix 4 For the chain 1cnvA, the alignment 1cnvA.msf (attached) with 152 4.1 File formats 4 sequences was used. The alignment was downloaded from the HSSP 4.2 Color schemes used 5 database, and fragments shorter than 75% of the query as well as 4.3 Credits 5 duplicate sequences were removed. It can be found in the attachment 4.3.1 Alistat 5 to this report, under the name of 1cnvA.msf. Its statistics, from the 4.3.2 CE 5 alistat program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 1-141 in 1cnvA colored by their relative importance. (See Appendix, Fig.7, for the coloring scheme.) Fig. 2. Residues 142-283 in 1cnvA colored by their relative importance. (See Appendix, Fig.7, for the coloring scheme.) Fig. 3. Residues in 1cnvA, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 152 Total number of residues: 40127 Smallest: 221 belong to. The clusters in Fig.4 are composed of the residues listed Largest: 283 Average length: 264.0 Alignment length: 283 Average identity: 46% Most related pair: 99% Most unrelated pair: 19% Most distant seq: 45% Furthermore, <1% of residues show as conserved in this ali- gnment. The alignment consists of 52% eukaryotic ( 6% fungi, 46% plan- tae) sequences. (Descriptions of some sequences were not readily available.) The file containing the sequence descriptions can be found in the attachment, under the name 1cnvA.descr. 2.3 Residue ranking in 1cnvA The 1cnvA sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues in 1cnvA can be found in the file called 1cnvA.ranks sorted in the attachment. 2.4 Top ranking residues in 1cnvA and their position on the structure In the following we consider residues ranking among top 25% of Fig. 4. Residues in 1cnvA, colored according to the cluster they belong to: residues in the protein . Figure 3 shows residues in 1cnvA 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. Table 2. continued cluster size member res type substitutions(%) cvg color residues N(1)S(1)E(1)T. red 67 11,12,13,17,19,23,31,35,36 39,40,62,69,72,73,76,79,81 Table 2. Residues forming surface ”patch” in 1cnvA. 82,84,85,90,98,102,105,106 110,112,116,117,118,119,121 123,124,125,127,128,129,130 Table 3. 131,146,159,160,161,162,163 res type disruptive 164,165,168,169,175,176,178 mutations 182,184,185,186,187,188,189 73 Q (Y)(T)(FW)(H) 190,191,225,228,237,265 124 D (R)(H)(FW)(Y) blue 3 259,260,261 123 L (R)(Y)(H)(TK) 106 H (E)(D)(Q)(M) Table 1. Clusters of top ranking residues in 1cnvA. 76 G (R)(K)(E)(Q) 110 L (R)(Y)(H)(T) 112 E (H)(FW)(Y)(R) 2.4.2 Possible novel functional surfaces at 25% coverage. One group of residues is conserved on the 1cnvA surface, away from (or Table 3. Disruptive mutations for the surface patch in 1cnvA. susbtantially larger than) other functional sites and interfaces reco- gnizable in PDB entry 1cnv. It is shown in Fig. 5. The right panel Another group of surface residues is shown in Fig.6. The right panel shows (in blue) the rest of the larger cluster this surface belongs to. shows (in blue) the rest of the larger cluster this surface belongs to. Fig. 5. A possible active surface on the chain 1cnvA. The larger cluster it Fig. 6. Another possible active surface on the chain 1cnvA. The larger cluster belongs to is shown in blue. it belongs to is shown in blue. The residues belonging to this surface ”patch” are listed in Table The residues belonging to this surface ”patch” are listed in Table 2, while Table 3 suggests possible disruptive replacements for these 4, while Table 5 suggests possible disruptive replacements for these residues (see Section 3.6). residues (see Section 3.6). Table 2. Table 4. res type substitutions(%) cvg res type substitutions(%) cvg antn 73 Q Q(96).K(1)RL 0.04 165 C C(100) 0.00 S-S 124 D D(92)N(5)GAE 0.08 168 P P(96)Q(1)DGFS 0.03 123 L L(71)V(25)I(1)T 0.12 169 D D(95).P(2)QS 0.03 M 189 Y Y(90)F(9) 0.03 106 H W(87)Y(5)F(2) 0.14 164 G Q(75)R(20)LK(1) 0.04 H(1)T(1)Q.(1) AG 76 G G(83)Y(1)DN(11) 0.16 187 R Q(76)R(19)K(2)E 0.05 .AHI N 110 L L(79)G(11)P(1) 0.20 265 W W(94)Y(2)D(1) 0.06 M(3)A(1)F(1). .(1)L 112 E G(88)R(1)V(2)P 0.22 35 F F(95)TY(1)Q.(1) 0.07 continued in next column continued in next column 3 Table 4. continued 3 NOTES ON USING TRACE RESULTS res type substitutions(%) cvg antn 3.1 Coverage 12 G G(96)R.(2) 0.12 131 Q E(74)D(17)A(1) 0.14 Trace results are commonly expressed in terms of coverage: the resi- Q(2)K(1)NL(1)GV due is important if its “coverage” is small - that is if it belongs to 17 G G(92)A(1)P(1)RK 0.15 some small top percentage of residues [100% is all of the residues YQE.(1) in a chain], according to trace. The ET results are presented in the 184 I V(66)I(23)A(9)L 0.17 form of a table, usually limited to top 25% percent of residues (or 190 N N(77)G(10)D(7) 0.17 to some nearby percentage), sorted by the strength of the presumed S(1)YE(1)K evolutionary pressure. (I.e., the smaller the coverage, the stronger the 13 Q Q(73)R(20)TE 0.18 pressure on the residue.) Starting from the top of that list, mutating a N(1)LM.(1) couple of residues should affect the protein somehow, with the exact 11 W W(94)Y(1)G.(2)R 0.19 effects to be determined experimentally. 237 G G(83)A(5)D(3) 0.19 .(3)Y(1)NTV 3.2 Known substitutions 178 T T(82)S(3)Q(3) 0.20 One of the table columns is “substitutions” - other amino acid types N(5).(1)KLE(1)G seen at the same position in the alignment. These amino acid types 176 I L(66)I(27)V(3)M 0.21 may be interchangeable at that position in the protein, so if one wants KF to affect the protein by a point mutation, they should be avoided.
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