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2Q8w Lichtarge Lab 2006 Pages 1–5 2q8w Evolutionary trace report by report maker July 1, 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 5 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 2q8w): Title: Crystal structure of pap-s1aci, a pokeweed antiviral protein from seeds of phytolacca acinosa Compound: Mol id: 1; molecule: pokeweed antiviral protein; chain: a; ec: 3.2.2.22 CONTENTS Organism, scientific name: Phytolacca Acinosa; 2q8w contains a single unique chain 2q8wA (261 residues long). 1 Introduction 1 2 Chain 2q8wA 1 2.1 Q8S947 overview 1 2.2 Multiple sequence alignment for 2q8wA 1 2.3 Residue ranking in 2q8wA 1 2.4 Top ranking residues in 2q8wA and their position on 2 CHAIN 2Q8WA the structure 1 2.1 Q8S947 overview 2.4.1 Clustering of residues at 25% coverage. 2 From SwissProt, id Q8S947, 95% identical to 2q8wA: 2.4.2 Possible novel functional surfaces at 25% Description: PAP-S1 (Fragment). coverage. 2 Organism, scientific name: Phytolacca americana (Common poke- berry) (Virginian pokeweed). 3 Notes on using trace results 3 Taxonomy: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; 3.1 Coverage 3 Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core 3.2 Known substitutions 3 eudicotyledons; Caryophyllales; Phytolaccaceae; Phytolacca. 3.3 Surface 4 3.4 Number of contacts 4 3.5 Annotation 4 3.6 Mutation suggestions 4 2.2 Multiple sequence alignment for 2q8wA 4 Appendix 4 For the chain 2q8wA, the alignment 2q8wA.msf (attached) with 70 4.1 File formats 4 sequences was used. The alignment was downloaded from the HSSP 4.2 Color schemes used 4 database, and fragments shorter than 75% of the query as well as 4.3 Credits 4 duplicate sequences were removed. It can be found in the attachment 4.3.1 Alistat 4 to this report, under the name of 2q8wA.msf. Its statistics, from the 4.3.2 CE 5 alistat program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 1-130 in 2q8wA colored by their relative importance. (See Appendix, Fig.6, for the coloring scheme.) Fig. 2. Residues 131-261 in 2q8wA colored by their relative importance. (See Appendix, Fig.6, for the coloring scheme.) Fig. 3. Residues in 2q8wA, colored by their relative importance. Clockwise: Format: MSF front, back, top and bottom views. Number of sequences: 70 Total number of residues: 17120 Smallest: 218 Largest: 261 Average length: 244.6 Alignment length: 261 Average identity: 33% Most related pair: 99% Most unrelated pair: 19% Most distant seq: 35% Furthermore, 2% of residues show as conserved in this alignment. The alignment consists of 77% eukaryotic ( 77% 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 2q8wA.descr. 2.3 Residue ranking in 2q8wA The 2q8wA sequence is shown in Figs. 1–2, with each residue colo- red according to its estimated importance. The full listing of residues in 2q8wA can be found in the file called 2q8wA.ranks sorted in the attachment. 2.4 Top ranking residues in 2q8wA and their position on Fig. 4. Residues in 2q8wA, 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 corresponding Pymol script is attached. residues in the protein . Figure 3 shows residues in 2q8wA colored by their importance: bright red and yellow indicate more conser- ved/important residues (see Appendix for the coloring scheme). A in Table 1. 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 2 Table 1. Table 2. continued cluster size member res type substitutions(%) cvg color residues 170 I V(4)I(94)L(1) 0.06 red 62 16,19,23,24,39,49,51,54,63 70 N N(74)D(22)S(2) 0.08 64,65,68,70,71,72,73,74,75 19 F F(90)L(4)S(1) 0.09 76,78,85,89,116,118,120,122 V(2).(1) 125,134,139,140,144,148,151 183 E E(75)S(2)Q(20) 0.10 163,165,166,167,169,170,171 G(1) 172,173,175,176,177,178,179 49 Y Y(50)F(38)L(7) 0.11 180,181,182,183,186,196,203 H(1)N(1)V(1) 204,205,207,210,211,214,250 181 Y Y(75)F(14)A(7) 0.12 251 I(1)H(1) 89 F F(67)Y(12)L(15) 0.13 Table 1. Clusters of top ranking residues in 2q8wA. P(2)S(1) 73 V L(12)I(7)V(77) 0.15 Y(2) 2.4.2 Possible novel functional surfaces at 25% coverage. One 172 M M(77)T(8)C(1) 0.16 group of residues is conserved on the 2q8wA surface, away from (or I(2)L(4)S(5) susbtantially larger than) other functional sites and interfaces reco- 63 T T(67)V(1)S(24) 0.17 gnizable in PDB entry 2q8w. It is shown in Fig. 5. The right panel E(2)Q(1)I(1) shows (in blue) the rest of the larger cluster this surface belongs to. K(1) 118 Y Y(58)F(34)I(2) 0.17 V(1).(1)C(1) 205 E K(2)N(51)E(21) 0.18 V(8)T(14)L(1) 68 R R(50)A(4)V(35) 0.20 M(1)L(2)K(5) 120 G K(2)G(50)S(27) 0.20 E(17)T(1).(1) 196 P P(71).(5)V(2) 0.20 S(11)K(4)C(1) A(2) 204 E E(78)Q(20)K(1) 0.22 51 L L(65)Y(7)F(4) 0.23 Fig. 5. A possible active surface on the chain 2q8wA. The larger cluster it R(12)H(1)V(5) belongs to is shown in blue. S(1)K(1) 180 K K(67)P(1)R(22) 0.23 T(4)E(1)Q(2) The residues belonging to this surface ”patch” are listed in Table 74 M E(4)W(4)V(48) 0.24 2, while Table 3 suggests possible disruptive replacements for these M(29)L(4)I(5) residues (see Section 3.6). A(2) Table 2. res type substitutions(%) cvg Table 2. Residues forming surface ”patch” in 2q8wA. 72 Y Y(100) 0.02 139 L L(100) 0.02 140 G G(100) 0.02 Table 3. 175 E E(100) 0.02 res type disruptive 178 R R(100) 0.02 mutations 207 W W(100) 0.02 72 Y (K)(QM)(NEVLAPIR)(D) 144 L L(97)I(2) 0.03 139 L (YR)(TH)(SKECG)(FQWD) 122 Y Y(98).(1) 0.04 140 G (KER)(FQMWHD)(NYLPI)(SVA) 24 R R(97).(1)H(1) 0.05 175 E (FWH)(YVCARG)(T)(SNKLPI) 182 I I(95)M(2)V(1) 0.05 178 R (TD)(SYEVCLAPIG)(FMW)(N) 134 R R(94)G(1).(2) 0.06 207 W (KE)(TQD)(SNCRG)(M) K(1) 144 L (YR)(TH)(SKECG)(FQWD) continued in next column 122 Y (K)(QM)(NVLAPI)(ER) continued in next column 3 Table 3. continued 3.3 Surface res type disruptive To detect candidates for novel functional interfaces, first we look for mutations residues that are solvent accessible (according to DSSP program) by 24 R (TD)(SEVCLAPIG)(YM)(FNW) 2 at least 10A˚ , which is roughly the area needed for one water mole- 182 I (Y)(R)(H)(T) cule to come in the contact with the residue. Furthermore, we require 134 R (D)(T)(Y)(SEVLAPI) that these residues form a “cluster” of residues which have neighbor 170 I (YR)(H)(T)(KE) within 5A˚ from any of their heavy atoms. 70 N (Y)(FWH)(R)(T) Note, however, that, if our picture of protein evolution is correct, 19 F (K)(E)(Q)(R) the neighboring residues which are not surface accessible might be 183 E (FWH)(YR)(VA)(CG) equally important in maintaining the interaction specificity - they 49 Y (K)(EQ)(MR)(N) should not be automatically dropped from consideration when choo- 181 Y (K)(Q)(E)(MR) sing the set for mutagenesis. (Especially if they form a cluster with 89 F (K)(E)(R)(Q) the surface residues.) 73 V (R)(K)(E)(Y) 172 M (Y)(H)(R)(T) 3.4 Number of contacts 63 T (R)(H)(FW)(K) Another column worth noting is denoted “noc/bb”; it tells the num- 118 Y (K)(Q)(ER)(M) ber of contacts heavy atoms of the residue in question make across 205 E (H)(FW)(Y)(R) the interface, as well as how many of them are realized through the 68 R (Y)(T)(D)(E) backbone atoms (if all or most contacts are through the backbone, 120 G (R)(FW)(H)(K) mutation presumably won’t have strong impact).
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