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1Gyd Lichtarge Lab 2006 Pages 1–7 1gyd Evolutionary trace report by report maker January 18, 2010 4.3.3 DSSP 6 4.3.4 HSSP 6 4.3.5 LaTex 6 4.3.6 Muscle 6 4.3.7 Pymol 6 4.4 Note about ET Viewer 6 4.5 Citing this work 6 4.6 About report maker 7 4.7 Attachments 7 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1gyd): Title: Structure of cellvibrio cellulosa alpha-l-arabinanase Compound: Mol id: 1; molecule: arabinan endo-1,5-alpha-l- arabinosidase a; chain: b; synonym: alpha-l-arabinanase, abn a, endo-1,5-alpha-l- arabinanase a; ec: 3.2.1.99; engineered: yes Organism, scientific name: Cellvibrio Japonicus; 1gyd contains a single unique chain 1gydB (315 residues long). 2 CHAIN 1GYDB 2.1 P95470 overview CONTENTS From SwissProt, id P95470, 99% identical to 1gydB: 1 Introduction 1 Description: Endo-a1,5-arabinanase (EC 3.2.1.99). Organism, scientific name: Cellvibrio japonicus. 2 Chain 1gydB 1 Taxonomy: Bacteria; Proteobacteria; Gammaproteobacteria; Pseu- 2.1 P95470 overview 1 domonadales; Pseudomonadaceae; Cellvibrio. 2.2 Multiple sequence alignment for 1gydB 1 2.3 Residue ranking in 1gydB 1 2.2 Multiple sequence alignment for 1gydB 2.4 Top ranking residues in 1gydB and their position on For the chain 1gydB, the alignment 1gydB.msf (attached) with 99 the structure 2 sequences was used. The alignment was downloaded from the HSSP 2.4.1 Clustering of residues at 25% coverage. 2 database, and fragments shorter than 75% of the query as well as 2.4.2 Possible novel functional surfaces at 25% duplicate sequences were removed. It can be found in the attachment coverage. 2 to this report, under the name of 1gydB.msf. Its statistics, from the alistat program are the following: 3 Notes on using trace results 5 3.1 Coverage 5 Format: MSF 3.2 Known substitutions 5 Number of sequences: 99 3.3 Surface 5 Total number of residues: 28097 3.4 Number of contacts 5 Smallest: 237 3.5 Annotation 5 Largest: 315 3.6 Mutation suggestions 5 Average length: 283.8 Alignment length: 315 4 Appendix 5 Average identity: 31% 4.1 File formats 5 Most related pair: 99% 4.2 Color schemes used 6 Most unrelated pair: 14% 4.3 Credits 6 Most distant seq: 31% 4.3.1 Alistat 6 4.3.2 CE 6 1 Lichtarge lab 2006 Fig. 1. Residues 33-189 in 1gydB colored by their relative importance. (See Appendix, Fig.7, for the coloring scheme.) Fig. 3. Residues in 1gydB, colored by their relative importance. Clockwise: front, back, top and bottom views. Fig. 2. Residues 190-347 in 1gydB colored by their relative importance. (See Appendix, Fig.7, for the coloring scheme.) Furthermore, <1% of residues show as conserved in this ali- gnment. The alignment consists of 8% eukaryotic ( 8% fungi), and 12% 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 1gydB.descr. 2.3 Residue ranking in 1gydB The 1gydB sequence is shown in Figs. 1–2, with each residue colored according to its estimated importance. The full listing of residues in 1gydB can be found in the file called 1gydB.ranks sorted in the attachment. 2.4 Top ranking residues in 1gydB 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 1gydB colored by their importance: bright red and yellow indicate more conser- ved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. Fig. 4. Residues in 1gydB, 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 2.4.1 Clustering of residues at 25% coverage. Fig. 4 shows the corresponding Pymol script is attached. 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 in Table 1. Table 1. cluster size member color residues continued in next column 2 Table 1. continued Table 2. continued cluster size member res type substitutions(%) cvg antn color residues 175 S S(89)G(1)E(1) 0.06 red 78 37,38,39,48,49,51,53,54,57 A(3)F(1).(2) 62,64,68,94,95,96,97,105,107 T(1)N(1) 108,109,112,115,119,121,122 37 H P(16)A(8)H(71) 0.07 124,138,140,142,155,156,157 .(3)D(1) 158,159,164,167,170,171,173 142 G G(86)P(2)L(1) 0.08 174,175,176,177,179,180,185 .(4)D(1)S(2) 221,222,232,233,234,235,237 N(1)I(1)K(1) 239,241,242,248,249,251,253 241 C C(77).(5)G(1) 0.09 S-S 254,255,256,261,262,263,265 L(8)T(4)A(3) 268,271,274,276,288,290,291 F(1) 306,329,330,331 222 A G(52)A(43)P(1) 0.10 S(1).(1)N(1) Table 1. Clusters of top ranking residues in 1gydB. 288 G G(77)A(7)E(2) 0.10 S(10).(3) 155 N N(84)G(4)E(4) 0.11 2.4.2 Possible novel functional surfaces at 25% coverage. One W(1)Q(2)R(1) group of residues is conserved on the 1gydB surface, away from (or D(1).(1)Y(1) susbtantially larger than) other functional sites and interfaces reco- 239 G G(69)D(23)S(1) 0.11 gnizable in PDB entry 1gyd. It is shown in Fig. 5. The right panel T(1)N(3)P(1) shows (in blue) the rest of the larger cluster this surface belongs to. R(1) 242 C C(77).(4)G(2) 0.12 S-S M(3)D(5)S(1) Q(1)W(2)N(1) A(3) 248 T T(48)G(10)P(2) 0.12 A(1)E(28)D(5) K(1)Q(1)S(2) R(1) 112 S S(78)V(2)Y(1) 0.13 R(4)C(4)A(2) H(1)N(3)T(2) G(1)I(1) 53 T A(12)T(67)G(7) 0.14 Fig. 5. A possible active surface on the chain 1gydB. The larger cluster it V(3).(5)S(2) belongs to is shown in blue. F(1)Y(2) 105 F Y(73)F(20)T(1) 0.14 W(1)V(3).(1) The residues belonging to this surface ”patch” are listed in Table 140 D D(79)Q(2)G(3) 0.15 2, while Table 3 suggests possible disruptive replacements for these A(2)K(1)E(2) residues (see Section 3.6). .(4)P(1)L(1) Table 2. V(2)N(2) 138 W F(16)W(66)Y(5) 0.16 res type substitutions(%) cvg antn R(2)H(1)N(1) 158 D D(100) 0.01 .(4)V(2)P(1) 249 Y Y(94)H(3)L(1) 0.01 S(1) E(1) 291 H H(56)G(29)P(2) 0.17 38 D D(98)P(1) 0.02 R(1).(3)Q(1) 96 P P(98)A(1) 0.02 V(4)M(1)A(1) 221 E E(97)Q(1).(1) 0.03 I(1) 94 W W(93)F(2)G(1) 0.04 54 G T(14)E(2)G(63) 0.18 L(1)Q(1)A(1) A(4)S(4)D(3) 157 I I(93)V(3)F(1) 0.04 L(2) continued in next column continued in next column 3 Table 2. continued Table 3. continued res type substitutions(%) cvg antn res type disruptive M(1)Q(2)H(4) mutations L(2) 291 H (E)(TD)(Q)(S) 159 P Q(4)P(68)A(18) 0.19 54 G (R)(K)(H)(E) G(9) 159 P (Y)(R)(H)(TE) 176 F F(62)Y(26)W(6) 0.20 176 F (K)(E)(QR)(T) N(1)D(2)T(1) 177 W (E)(K)(D)(T) P(1) 97 D (R)(H)(FW)(K) 177 W R(7)H(5)W(54) 0.21 115 G (R)(K)(H)(E) .(4)F(14)G(4) 106 Y (K)(Q)(E)(R) S(5)N(3)I(1) L(2) Table 3. Disruptive mutations for the surface patch in 1gydB. 97 D D(69)V(1)N(2) 0.23 T(5)E(8)F(1) Another group of surface residues is shown in Fig.6. The right panel H(3)Y(2)A(1) shows (in blue) the rest of the larger cluster this surface belongs to. S(1)M(2)Q(4) 115 G G(78)D(5)S(3) 0.23 E(1)A(3)K(2) N(2).(1)Y(1) L(1)I(1)P(1) 106 Y V(13)Y(55)W(6) 0.25 H(9)R(5)S(1) F(1)L(4).(2) M(1)I(2) Table 2. Residues forming surface ”patch” in 1gydB. Table 3. res type disruptive Fig.
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